evolution of pallium, hippocampus, and cortical cell types … · fig. 1e and fig. 2b), in...

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NEURODEVELOPMENT Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles Maria Antonietta Tosches,*Tracy M. Yamawaki,*Robert K. Naumann,§ Ariel A. Jacobi,Georgi Tushev, Gilles LaurentComputations in the mammalian cortex are carried out by glutamatergic and g-aminobutyric acidreleasing (GABAergic) neurons forming specialized circuits and areas. Here we asked how these neurons and areas evolved in amniotes.We built a gene expression atlas of the pallium of two reptilian species using large-scale single-cell messenger RNA sequencing. The transcriptomic signature of glutamatergic neurons in reptilian cortex suggests that mammalian neocortical layers are made of new cell types generated by diversification of ancestral gene-regulatory programs. By contrast, the diversity of reptilian cortical GABAergic neurons indicates that the interneuron classes known in mammals already existed in the common ancestor of all amniotes. A mniote vertebrates (mammals, reptiles, and birds) originated from a common an- cestor about 320 million years ago. In all developing amniotes, the dorsal telence- phalon, or pallium, is patterned by the same signaling molecules and subdivided in homol- ogous embryonic regions (1). In adult amniote brains, however, the structures that arise from these homologous pallial regions have different morphologies and connectivity. For example, a six-layered neocortex exists only in mammals, and the dorsal ventricular ridge (DVR) is found only in birds and reptiles. The hippocampus may be the most conserved pallial region (2), but even there, it is uncertain whether all the subfields known in mammals (for example, the dentate gyrus) exist in nonmammals (3) (fig. S1). Gene expression data can help reconstruct the evolution of brain regions and cell types (4, 5). Here we used single-cell transcriptomics to study the evolution of neuronal diversity in the am- niote telencephalon. Because cell types defined through transcriptomics match those defined by morphology, physiology, and connectivity (68), single-cell mRNA sequencing can be applied both for cell-type discovery and for cross-species comparisons (9). We focused on reptiles, because they, unlike birds, have a layered cortex, and asked the following: (i) Can we identify molecular sim- ilarities and homologies between reptilian and mammalian pallial regions? (ii) Are there rep- tilian cortical neurons homologous to mamma- lian hippocampal neurons? (iii) Can we link the reptilian three-layered cortex to the mamma- lian six-layered neocortex? (iv) Are mammalian g-aminobutyric acidreleasing (GABAergic) inter- neuron types also found in the reptilian cortex? Neuronal and glial cells in the reptilian pallium Using Drop-seq (8), we obtained a comprehen- sive, unbiased classification of adult cell types sampled from the pallium of a turtle and a lizard species (dissections and sequencing statistics in figs. S1 and S2 and tables S1 and S2). After quality filtering (fig. S3), we used unsupervised graph-based clustering of the transcripts from 18,828 turtle and 4187 lizard cells (with a median of 2731.5 and 1918 transcripts per cell, respec- tively) and identified first-level clusters of neu- ronal and non-neuronal cells (Fig. 1, A to C). Among non-neuronal cells, we found clusters expressing prototypical markers of mammalian glial cells: mature oligodendrocytes and their precursors, ependymoglial cells, and microglia (Fig. 1, B to D). Ependymoglial cells coexpressed markers of mammalian astrocytes (GFAP), adult stem cells (SOX9), and ependymal cells (FOXJ1), suggesting a shared evolutionary origin of these cell types (fig. S4, A to C). Reptilian neuronal clusters included vesicular glutamate transporter type 1 (VGLUT1 + ) glutamatergic excitatory neu- rons, glutamate decarboxylase 1 and 2 (GAD1 + GAD2 + ) GABAergic inhibitory interneurons, and neural progenitor cells (Fig. 1, A to D), con- sistent with the existence of adult neurogenesis in reptiles. To compare the transcriptomes of turtle, lizard, and mouse neuronal and non- neuronal cells (6), we selected one-to-one ortho- logs differentially expressed among these cell types, defined a specificity score for each gene in each cluster, and computed pairwise rank cor- relations (see methods). This analysis supports correspondence between major neuronal and non-neuronal cell classes (fig. S4, D to F) across turtle, lizard, and mouse. Subclustering of the turtle and lizard neurons revealed finer distinctions between and within excitatory glutamatergic and inhibitory GABAergic neuron types (Fig. 1, E to G, and fig. S5). From these neuronal data sets, we selected differentially expressed genes as markers for histological vali- dation and for unbiased comparisons with mam- malian cell types. We focused on the turtle data and used the lizard data for corroboration. Spatial segregation of glutamatergic neurons: A molecular map of the reptilian pallium Our dissections encompassed multiple regions of the reptilian pallium likely to contain hetero- geneous populations of glutamatergic neurons. To establish the anatomical location of our turtle glutamatergic-cell clusters, we selected highly variable genes in the data set that were ex- pressed in some clusters but not detected in others. These markers were expressed in distinct regions of the pallium (fig. S6). The combinato- rial expression of markers defined superclus- ters,seen also as groupings of adjacent clusters in t-distributed stochastic neighbor embedding (tSNE) plots (Fig. 2, A to B, and fig. S6A; compare Fig. 1E and Fig. 2B), in agreement with higher- level clustering analysis and with our tissue dis- sections (figs. S7 and S8D and tables S1 and S2). These superclusters correspond to defined ana- tomical regions: the medial and dorsomedial cortices, the anterior and posterior dorsal cortex, the pallial thickening, the anterior and poste- rior lateral cortex, and the anterior and poste- rior DVR (fig. S8, A to C). Cell-type similarity was generally higher within than between superclus- ters (fig. S8, F and G). Weighted gene correlation network analysis (WGCNA, see methods) indi- cates that the unique genetic signature of each region results from different combinations of gene modules (Fig. 2C). We also associated gluta- matergic clusters to anatomically defined pallial regions in lizard (fig. S9). Corresponding regions in lizard and turtle have different relative sizes (for example, lizard anterior dorsal cortex is small) but are clearly delineated by the expression of the same developmental transcription factors such as ZBTB20, SATB1, DACH2, and ETV1 (ER81) (Fig. 2D). These data define the molecular regionaliza- tion of the adult reptilian pallium. Putative homologies between reptilian and mammalian pallial derivatives are disputed (1, 2, 10, 11). Central to this debate is the an- terior DVR, one of the derivatives of the ventral pallium, which is enlarged in birds and reptiles. This region has been proposed as a homolog of either ventral pallium derivatives [claus- trum, endopiriform nucleus, and pallial amyg- dala (1, 2, 12)] or parts of the neocortex in mammals (5, 10, 11). The latter hypothesis sug- gests a dual evolutionary origin of the neocortex, either as separate regionswhere medial and lateral neocortex are homologous to reptilian dorsal cortex and DVR, respectively (11)or as intermixed cell types, where separate neocortical layers are homologous to reptilian dorsal cortex or DVR ( 5, 10). We compared the turtle superclusters RESEARCH Tosches et al., Science 360, 881888 (2018) 25 May 2018 1 of 8 Max Planck Institute for Brain Research, Max-von-Laue Strasse 4, 60438 Frankfurt am Main, Germany. *These authors contributed equally to this work. Corresponding author. Email: [email protected] (G.L.); [email protected] (M.A.T.) Present address: Amgen, Inc., 1120 Veterans Blvd., South San Francisco, CA 94080, USA. §Present address: Shenzhen Institutes of Advanced Tech- nology, Chinese Academy of Sciences, 1068 Xueyuan Ave., Shenzhen University Town, Nanshan District, 518055 Shenzhen, China. ||Present address: University of California, Davis, School of Medicine, 4610 X St., Sacramento, CA 95817, USA. on November 20, 2020 http://science.sciencemag.org/ Downloaded from

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Page 1: Evolution of pallium, hippocampus, and cortical cell types … · Fig. 1E and Fig. 2B), in agreement with higher-level clustering analysis and with our tissue dis-sections (figs

NEURODEVELOPMENT

Evolution of pallium, hippocampus,and cortical cell types revealed bysingle-cell transcriptomics in reptilesMaria Antonietta Tosches,*† Tracy M. Yamawaki,*‡ Robert K. Naumann,§Ariel A. Jacobi,‖ Georgi Tushev, Gilles Laurent†

Computations in the mammalian cortex are carried out by glutamatergic and g-aminobutyricacid–releasing (GABAergic) neurons forming specialized circuits and areas. Here weasked how these neurons and areas evolved in amniotes. We built a gene expressionatlas of the pallium of two reptilian species using large-scale single-cell messenger RNAsequencing. The transcriptomic signature of glutamatergic neurons in reptilian cortexsuggests that mammalian neocortical layers are made of new cell types generated bydiversification of ancestral gene-regulatory programs. By contrast, the diversity of reptiliancortical GABAergic neurons indicates that the interneuron classes known in mammalsalready existed in the common ancestor of all amniotes.

Amniote vertebrates (mammals, reptiles,and birds) originated from a common an-cestor about 320 million years ago. In alldeveloping amniotes, the dorsal telence-phalon, or pallium, is patterned by the same

signaling molecules and subdivided in homol-ogous embryonic regions (1). In adult amniotebrains, however, the structures that arise fromthese homologous pallial regions have differentmorphologies and connectivity. For example,a six-layered neocortex exists only in mammals,and the dorsal ventricular ridge (DVR) is foundonly in birds and reptiles. The hippocampus maybe the most conserved pallial region (2), but eventhere, it is uncertain whether all the subfieldsknown in mammals (for example, the dentategyrus) exist in nonmammals (3) (fig. S1).Gene expression data can help reconstruct the

evolution of brain regions and cell types (4, 5).Here we used single-cell transcriptomics to studythe evolution of neuronal diversity in the am-niote telencephalon. Because cell types definedthrough transcriptomics match those defined bymorphology, physiology, and connectivity (6–8),single-cell mRNA sequencing can be appliedboth for cell-type discovery and for cross-speciescomparisons (9). We focused on reptiles, becausethey, unlike birds, have a layered cortex, and askedthe following: (i) Can we identify molecular sim-ilarities and homologies between reptilian andmammalian pallial regions? (ii) Are there rep-tilian cortical neurons homologous to mamma-lian hippocampal neurons? (iii) Can we link the

reptilian three-layered cortex to the mamma-lian six-layered neocortex? (iv) Are mammaliang-aminobutyric acid–releasing (GABAergic) inter-neuron types also found in the reptilian cortex?

Neuronal and glial cells in thereptilian pallium

Using Drop-seq (8), we obtained a comprehen-sive, unbiased classification of adult cell typessampled from the pallium of a turtle and a lizardspecies (dissections and sequencing statisticsin figs. S1 and S2 and tables S1 and S2). Afterquality filtering (fig. S3), we used unsupervisedgraph-based clustering of the transcripts from18,828 turtle and 4187 lizard cells (with a medianof 2731.5 and 1918 transcripts per cell, respec-tively) and identified first-level clusters of neu-ronal and non-neuronal cells (Fig. 1, A to C).Among non-neuronal cells, we found clustersexpressing prototypical markers of mammalianglial cells: mature oligodendrocytes and theirprecursors, ependymoglial cells, and microglia(Fig. 1, B to D). Ependymoglial cells coexpressedmarkers of mammalian astrocytes (GFAP), adultstem cells (SOX9), and ependymal cells (FOXJ1),suggesting a shared evolutionary origin of thesecell types (fig. S4, A to C). Reptilian neuronalclusters included vesicular glutamate transportertype 1 (VGLUT1+) glutamatergic excitatory neu-rons, glutamate decarboxylase 1 and 2 (GAD1+

GAD2+) GABAergic inhibitory interneurons, andneural progenitor cells (Fig. 1, A to D), con-sistent with the existence of adult neurogenesisin reptiles. To compare the transcriptomes ofturtle, lizard, and mouse neuronal and non-neuronal cells (6), we selected one-to-one ortho-logs differentially expressed among these celltypes, defined a specificity score for each genein each cluster, and computed pairwise rank cor-relations (see methods). This analysis supportscorrespondence between major neuronal andnon-neuronal cell classes (fig. S4, D to F) acrossturtle, lizard, and mouse.

Subclustering of the turtle and lizard neuronsrevealed finer distinctions between and withinexcitatory glutamatergic and inhibitory GABAergicneuron types (Fig. 1, E to G, and fig. S5). Fromthese neuronal data sets, we selected differentiallyexpressed genes as markers for histological vali-dation and for unbiased comparisons with mam-malian cell types. We focused on the turtle dataand used the lizard data for corroboration.

Spatial segregation of glutamatergicneurons: A molecular map of thereptilian pallium

Our dissections encompassed multiple regionsof the reptilian pallium likely to contain hetero-geneous populations of glutamatergic neurons.To establish the anatomical location of our turtleglutamatergic-cell clusters, we selected highlyvariable genes in the data set that were ex-pressed in some clusters but not detected inothers. These markers were expressed in distinctregions of the pallium (fig. S6). The combinato-rial expression of markers defined “superclus-ters,” seen also as groupings of adjacent clustersin t-distributed stochastic neighbor embedding(tSNE) plots (Fig. 2, A to B, and fig. S6A; compareFig. 1E and Fig. 2B), in agreement with higher-level clustering analysis and with our tissue dis-sections (figs. S7 and S8D and tables S1 and S2).These superclusters correspond to defined ana-tomical regions: the medial and dorsomedialcortices, the anterior and posterior dorsal cortex,the pallial thickening, the anterior and poste-rior lateral cortex, and the anterior and poste-rior DVR (fig. S8, A to C). Cell-type similarity wasgenerally higher within than between superclus-ters (fig. S8, F and G). Weighted gene correlationnetwork analysis (WGCNA, see methods) indi-cates that the unique genetic signature of eachregion results from different combinations ofgene modules (Fig. 2C). We also associated gluta-matergic clusters to anatomically defined pallialregions in lizard (fig. S9). Corresponding regionsin lizard and turtle have different relative sizes(for example, lizard anterior dorsal cortex is small)but are clearly delineated by the expression of thesame developmental transcription factors such asZBTB20, SATB1, DACH2, and ETV1 (ER81) (Fig.2D). These data define the molecular regionaliza-tion of the adult reptilian pallium.Putative homologies between reptilian and

mammalian pallial derivatives are disputed(1, 2, 10, 11). Central to this debate is the an-terior DVR, one of the derivatives of the ventralpallium, which is enlarged in birds and reptiles.This region has been proposed as a homologof either ventral pallium derivatives [claus-trum, endopiriform nucleus, and pallial amyg-dala (1, 2, 12)] or parts of the neocortex inmammals (5, 10, 11). The latter hypothesis sug-gests a dual evolutionary origin of the neocortex,either as separate regions—where medial andlateral neocortex are homologous to reptiliandorsal cortex and DVR, respectively (11)—or asintermixed cell types, where separate neocorticallayers are homologous to reptilian dorsal cortex orDVR (5, 10). We compared the turtle superclusters

RESEARCH

Tosches et al., Science 360, 881–888 (2018) 25 May 2018 1 of 8

Max Planck Institute for Brain Research, Max-von-LaueStrasse 4, 60438 Frankfurt am Main, Germany.*These authors contributed equally to this work.†Corresponding author. Email: [email protected](G.L.); [email protected] (M.A.T.) ‡Present address:Amgen, Inc., 1120 Veterans Blvd., South San Francisco, CA 94080,USA. §Present address: Shenzhen Institutes of Advanced Tech-nology, Chinese Academy of Sciences, 1068 Xueyuan Ave.,Shenzhen University Town, Nanshan District, 518055 Shenzhen,China. ||Present address: University of California, Davis, School ofMedicine, 4610 X St., Sacramento, CA 95817, USA.

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to mammalian pallial derivatives, using a humanmicroarray data set as a reference [(13); see anal-ysis in methods].Our analysis using all differentially expressed

genes (Fig. 2E) reveals similarities between tur-tle medial and dorsomedial cortices and humanhippocampus, supporting previous hypotheses(3). The posterior dorsal cortex also showed posi-tive correlations to human hippocampus andsubiculum but low negative correlations withnonhippocampal cortices, consistent with thegene network analysis (Fig. 2C). Earlier studiesrecognized anatomical similarities between partsof the reptilian dorsal cortex and mammaliansubiculum (2, 14), where ETV1 (ER81) is expressed(15). It may thus be that the posterior dorsalcortex relates to mammalian peri-hippocampalregions.Turtle pallial thickening and mammalian claus-

trum shared expression of several claustrum-enriched markers (fig. S6B), consistent withanatomical and developmental data (1, 2). Wealso found correlations between reptilian lateralcortex and mammalian piriform cortex andbetween posterior DVR and pallium-derivedamygdalar nuclei, with the exception of the lat-eral amygdala. Individual posterior DVR clustersexpressed markers of mammalian basolateral(ETV1 and FEZF2) and cortical (ZIC2 and TBR1)amygdala. These clusters mapped to distinctnuclei of the turtle posterior DVR, suggestingthat these pallial amygdala subdivisions existedin the common ancestor of mammals and rep-tiles (fig. S10) (16).Mammalian neocortex showed correlations

with several turtle pallial regions (Fig. 2E). Rea-soning that correlations based on all differentiallyexpressed genes might not separate homology

Tosches et al., Science 360, 881–888 (2018) 25 May 2018 2 of 8

pvEG

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SYT1 146.8

CPLX1 68.33

VGLUT1 19.93

CAMK2A 69.62

GAD1 128.8

GAD2 78.94

SOX4 106.9

SOX11 83.10

OLIG1 136.7

PDGFRA 65.95

MBP 289.4

GFAP 34.66

SOX9 133.2

C1QC 62.13

IGHG1 111.5

CXCR6 11.49

LUM 65.40

TBX18 16.63

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SYT1 171.9

CPLX1 125.9

VGLUT1 58.53

CAMK2A 70.12

GAD1 102.3

GAD2 81.33

SOX4A 61.40

SOX11 45.13

OLIG1 65.42

PDGFRA 59.43

MBP 493.0

GFAP 68.89

SOX9 69.15

C1QC 115.7

LUM 86.23

TBX18 13.49

SOX18 20.43

IGHG1 2936

CXCR6 29.06

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Fig. 1. Reptilian single-cell data sets.(A) tSNE representation of 18,828 turtle(Trachemys scripta elegans, ts) single-celltranscriptomes, with cells color coded by cluster.(B) Violin plots showing expression of neuronaland non-neuronal markers in turtle clusters.(C) tSNE representation of 4187 lizard (Pogonavitticeps, pv) single-cell transcriptomes, colorcoded by cluster. (D) Violin plots showingexpression of neuronal and non-neuronal markersin lizard clusters. In (B) and (D), for each gene,violin plots are scaled to the maximum numberof transcripts (unique molecule identifiers)detected for that gene (max). Exc, glutamatergicexcitatory neurons; Inh, GABAergic inhibitoryinterneurons; NPC, neural progenitor cells; Olig,mature oligodendrocytes; OPC, oligodendrocyteprecursors; EG, ependymoglial cells; MG, microglia;Leu, leucocytes; Mur, mural cells; Vend, vascularendothelial cells. Subclusters of Exc and Inh cells in(A) and (C) are not matched by name or color.(E) tSNE plot and clusters of 5901 high-qualityturtle neurons. Inset is the tSNE plot in (A),indicating neuronal and glial clusters in dark redand gray, respectively. (F and G) Expression ofthe glutamatergic marker VGLUT1 (F) andGABAergic marker GAD1 (G) in turtle neurons.

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from convergent evolution (because functionalconvergence could recruit the same effectorgenes under different transcription factors), wenext restricted our analysis to transcription fac-tors. Under these conditions, only anterior dorsalcortex correlated with human neocortex (Fig.2F). Anterior dorsal cortex and anterior DVRdiffered by the expression of those transcriptionfactors that, in mammals, are also found in eitherthe neocortex or pallial amygdala (for example,NFIX, BCL11A, and SATB2 in turtle anterior dorsalcortex and mouse neocortex; NR2F2 and DACH2in turtle anterior DVR and mouse amygdala) (fig.S8, H and I). Of the mammalian pallial amyg-dala subdivisions, only the lateral amygdala corre-lates with the anterior DVR. Our results suggestthat (i) different combinations of transcriptionfactors may regulate the expression of “neo-cortical” effector genes in anterior dorsal cortexand anterior DVR and (ii) transcription-factorexpression reflects the developmental (and evo-lutionary) history of pallial neurons. We proposethat reptilian anterior dorsal cortex and mam-malian neocortex are homologous as dorsalpallium derivatives and that reptilian DVR andmammalian pallial amygdala are homologousas ventral pallium derivatives [see also (1)]. Inreptiles, the expansion of the sensory-recipientanterior DVR led to the emergence of neuronaltypes specialized in processing different sensorymodalities, recognizable as separate molecular,anatomical, and functional clusters (figs. S9 andS10) (17). According to this hypothesis, reptiliananterior DVR and mammalian neocortex ac-quired, by convergent evolution, the expressionof similar sets of effector genes.

Conservation of hippocampal neuronaltypes and areal organization

Anatomical and developmental evidence suggestthat the reptilian medial-most cortex is homol-ogous to mammalian hippocampus (3, 18). Inline with this, turtle and lizard medial corticesexpress the mammalian pan-hippocampal tran-scription factor ZBTB20 (Fig. 3A and fig. S11).Whether individual hippocampal subfields [den-tate gyrus (DG), cornu ammonis (CA)3, CA2, andCA1] are present in reptiles and birds is less clear.Developmental evidence suggests so (18), but somedescribe mammalian DG, with its mossy cellsand granule cells, as a mammalian novelty (3).Reptilian ZBTB20-positive clusters could be

further distinguished by the expression of mam-malian DG or CA transcription factors: In turtle,PROX1 andMEF2C (specifying mouse DG granulecells) labeled the medial cortex, and ETV1,MEIS2,and LMO4 (CA) labeled the dorsomedial cortex(Fig. 3A). The expression of these genes in ad-jacent domains of turtle and lizard medial cor-tices (fig. S11) suggests the existence of DG- andCA-like neuronal types in reptiles. This was fur-ther supported by unbiased analyses of cell-typetranscriptomes. Using WGCNA to identify andcompare gene modules [mouse data from (19),see methods], we found statistically significantoverlaps between mouse DG and turtle medialcortex modules and between mouse CA and

turtle dorsomedial cortex modules (fig. S12).Mouse DG and turtle medial cortex modulesshared genes coding for K+-channel subunitsor associated proteins (KCNG1, KCNA1, andKCNIP4), possibly accounting for electrophysiolog-ical similarities (20). Other shared genes includedthe cadherin CDH8, involved in the formation ofDG-CA3 synapses, and the granule-cell specificregulators of synaptogenesis and AMPA receptor–mediated synaptic transmission LRRTM4 andCNIH3 (fig. S12). Hence, DG granule cells, in-cluding aspects of their membrane and synapticphysiology, are conserved across mammals andreptiles (20). [No mossy-cell marker (21) had cell-type specific expression in turtle medial cortex.]Next, we computed pairwise cluster correla-

tions using one-to-one orthologs differentially ex-pressed among the ZBTB20+ clusters. This revealedfurther heterogeneity among the ZBTB20+ ETV1+

cells, with turtle dorsomedial cortex clusters show-ing best mutual correlations to mouse CA3 or CA1(Fig. 3B). Mammalian CA3 or CA1 markers (19, 21)were differentially expressed in these turtle clus-ters (Fig. 3C). CA3- and CA1-like cells occupy ad-jacent positions [with CA3-like cells closest tomedial cortex (DG)] and form morphologicallydistinct cell plates (Fig. 3A and fig. S11). Wefound no evidence for a reptilian CA2 cell type(Fig. 3B and fig. S11B).In summary, reptilian hippocampus can be

subdivided into adjacent territories similar tothe mammalian DG, CA3, and CA1 fields. Thedevelopmental origin of these cells from themedial pallium (18) and their similar medio-lateral distribution, connections (22), biophysicalproperties (20), and molecular identities (thisstudy) support the hypothesis that mammalian-like hippocampal regions were already presentas adjacent fields in the ancestor of all amniotes.The architecture of the mammalian hippocam-pus, with its signature infoldings, may thus resultfrom the considerable enlargement of neocortexin the mammalian lineage.

Transcriptomic signatures ofneocortical upper and deep layersin turtle dorsal cortex

Mammalian six-layered neocortex evolved froma presumed three-layered ancestral cortex in astem amniote. What is the relationship betweenthe neurons and layers in the mammalian neo-cortex and the reptilian cortex? Earlier studiessuggested that L2/3 and L4 (“upper layer,” UL)neurons are mammalian novelties; reptilianpyramidal neurons have thus been comparedto the mammalian early born L5 and L6 (“deeplayer,” DL) neurons (23, 24). By contrast, con-nectivity implies that reptilian cortex shouldharbor both L4 (that is, thalamorecipient) andL5 (cortico-fugal) types, and it has been suggestedthat these types, rather than occupying differentlayers, populate adjacent fields in turtle cortex:one in anterior dorsal cortex (RORB+ L4-like neu-rons) and one in posterior dorsal cortex (ETV1+

L5-like neurons) (5, 10).Our data indicate that anterior dorsal cortex

is the only region comparable to mammalian neo-

cortex (Fig. 2). We examined the expression ofprototypical mammalian-layer markers (7, 25, 26)in the six turtle anterior dorsal cortex gluta-matergic clusters (e07, e08, and e13 to e16). Thesecells expressed several mammalian UL and DLmarkers, but these genes were often coexpressedin the same clusters (Fig. 4A and fig. S13A). Whenwe focused on the transcription factors that es-tablish and maintain cell identity in the neo-cortex, we observed that, in the turtle, these geneswere expressed in combinations that were neverobserved in differentiated mammalian corticalneurons. For example, all turtle anterior dorsalcortex cell types coexpress genes enriched inmammalian L2/3, L4, and L5a intratelencephalicneurons, including SATB2, RORB, and RFX3, aswell as genes specifying L5b and L6 corticofugalprojection neurons, such as BCL11B (CTIP2), TBR1,and SOX5 (all clusters except e13) (25) (Fig. 4,A and B). In mouse neocortex, some of thesegenes are known to repress each other’s expres-sion in postmitotic cells (for example, Satb2 andBcl11b; Tbr1 and Bcl11b) (26).Extending the comparative analysis to all dif-

ferentially expressed genes revealed that anteriordorsal cortex cell types correlated with eithermammalian UL (e13 to e16) or DL (e07 and e08)neurons, independent of the neocortical areaused for comparison (Fig. 4C and fig. S14, A toC). This trend was confirmed by gene networkanalysis (fig. S13, B and C). By contrast, anteriorDVR clusters could not be grouped into UL- andDL-like classes (fig. S14, D to F).As anticipated by the sequencing data, in situ

hybridizations (ISHs) showed coexpression ofmammalian UL and DL transcription factorsthroughout the turtle anterior dorsal cortex(Fig. 4B). Individual UL-like neuronal types (e13to e16) were differentially distributed along themediolateral and rostrocaudal axes of the anteriordorsal cortex, matching known anatomical sub-divisions (fig. S15). By contrast, the DL-like cellse07 and e08, identified by parathyroid hormone–like hormone (PTHLH) expression, appeared in-terspersed throughout the anterior dorsal cortex.In the rostro-lateral dorsal cortex, DL-like cellswere confined to the superficial part of L2 (Fig.4D; additional markers in fig. S15, C to E). Thesemarkers thus identify two distinct sublayers inturtle L2: a superficial L2a with mostly DL-likeneurons and a deeper L2b with mostly UL-likeneurons. Retrograde tracing from the thalamuslabels L2a cells (27, 28), suggesting that theseneurons, or a subset of them, are corticofugaland project to the thalamus.In conclusion, our transcriptome-wide com-

parisons reveal the presence of global UL- andDL-like genetic signatures in distinct neuronaltypes of turtle anterior dorsal cortex but do notsupport, with the current resolution, homologiesbetween turtle glutamatergic types and indi-vidual neocortical layers. In reptiles and mam-mals, UL and DL genetic signatures might haveevolved independently from a stem amniote thatlacked distinct UL- and DL-like neurons: Neu-rons with similar characteristics, such as input-output connectivity, would have acquired the

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expression of similar gene sets by convergentevolution. Alternatively, UL- and DL-like neuronsmay have existed already in the dorsal cortex ofstem amniotes. If true, the emergence of the sixlayers that form mammalian neocortex wouldbe a novelty [sensu (29)], with the evolution ofnew pyramidal cell types through extensive mod-ifications of the genetic programs specifying an-cestral UL- and DL-like types.

Conservation of GABAergic interneuronclasses across amniotes

GABAergic interneurons in mammalian neo-cortex are diverse and participate in differentcircuit motifs and computations (30). Little isknown about cortical interneurons outside ofmammals. In several vertebrates, including rep-tiles, GABAergic interneurons are generated inconserved subpallial regions—the medial, cau-dal, and lateral ganglionic eminences (MGE, CGE,and LGE)—and migrate to the pallium (31, 32).Reptiles, however, are thought to lack some mam-malian GABAergic types, such as cortical vaso-active intestinal peptide (VIP) interneurons (24).We examined the turtle GABAergic clusters (i01to i18) and the expression of transcription factorsknown to define mammalian GABAergic types.

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−0.41

0

0.55

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0

0.21

MCDMCpDCaDC

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BM

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all genes

neocortex

human (Hawrylycz et al 2012)

pallial amygdala

Correlation

Correlation

ET

V1

DMC

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DMC

pDC

pDVR

SA

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1

aDC

aDVR

aDC

aDVR

DA

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2

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−0.15

moduleeigengene(Z-score)

0

0.15

e29

e30

e31

e32

e33

e34

e35

e36

e37

e38

e24

e26

e27

e28

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e14

e15

e16

e07

e08

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e04

e05

e06

e09

e10

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e12

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e02

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e18

e17

e20

e21

e22

e23

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gene

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ules B

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F

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aDC

aDC

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B

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F

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max

6.999

23.28

30.75

85.61

45.12

23.94

16.12

14.37

10.04

65.86

11.97

21.35

306.3

11.74

5.567

80.32

ZBTB20PROX1

ETV1PENKWFS1

RORBFOXP1

NRP2KAL1TAC1

DACH2NR2F2

VLGUT1

ZIC2

SATB2SATB1

LGALS1

MC

DM

CpD

CaD

C PT

aLC

pLC

aDV

RpD

VR

Fig. 2. Reptilian pallial regions. (A) Violinplots showing expression of genes discrimi-nating between spatially segregated glutama-tergic neurons in the turtle pallium. (B) tSNEshowing turtle glutamatergic neurons coloredby supercluster. Transcription factor names arein red. (C) Heatmap showing expression ofmodule eigengenes calculated from turtleglutamatergic neurons. Pseudocells (averagesof 4 to 5 cells used for WGCNA, see methods)are shown in columns, ordered by cluster andsupercluster. (D) Expression of transcriptionfactors that label corresponding pallialregions in turtle and lizard (ISH, frontal sectionsat different anterior-posterior levels; seealso figs. S8 and S9). Scale bars, 1 mm.(E and F) Pairwise correlations of turtle gluta-matergic superclusters and human pallialregions, calculated from all genes (E) ortranscription factors (F) differentially expressedin turtle or human. In mammals, only someparts of the cingulate gyrus (CgG), long insulargyrus (LIG), and short insular gyrus (SIG) areclassified as neocortex [see (13) for humandata]. Dots indicate statistically significant cor-relations. MC, medial cortex; DMC, dorsomedialcortex; pDC and aDC, posterior and anteriordorsal cortex; PT, pallial thickening; aLC and pLC,anterior and posterior lateral cortex; aDVR andpDVR, anterior and posterior dorsal ventricularridge; DG, dentate gyrus; CA, cornu ammonis;Sub, subiculum; PHG, parahippocampal gyrus;OL, occipital lobe; TL, temporal lobe; PL, parietallobe; FL, frontal lobe; Cl, claustrum; Pir, piriformcortex; LA, lateral amygdala; ATZ, amygdalohip-pocampal transition zone; BLA, basolateralamygdala; BMA, basomedial amygdala; COMA,corticomedial amygdala.

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From the combinatorial expression of these genes,we identified putative MGE-derived (i07 to i13:LHX6+, SOX6+, and SATB1+), CGE-derived (i14 toi18: NPAS1+, SP8+, NR2E1+, and PROX1+), and LGE-derived (i01 and i04 to i06: MEIS2+ ZIC1– andin subsets TSHZ1+ SIX3+ and/or PBX3+) clusters(Fig. 5A). Corresponding MGE-, CGE-, and LGE-derived neurons could also be identified in liz-ard (fig. S16, A to C). The remaining GABAergicclusters correspond to cells dissected from theneighboring septum (i02 and i03) and striatum(i04). Stainings revealed the presence of LGE-and septum-derived interneurons in the amyg-dala (i04 and i05) and olfactory bulb (i01 andi02), indicating that LGE- and septum-derivedGABAergic neurons have similar molecular iden-

tities and migratory trajectories in reptiles andmammals (Fig. 5A and fig. S16, D and E).Turtle MGE- and CGE-derived interneurons

could be further subdivided into somatostatin(“SST”), parvalbumin-like (“PV-like”), “HTR3AReln,” and “HTR3A VIP-like” classes, match-ing the classification of mammalian corticalGABAergic interneurons (7, 30) (Fig. 5A). Pair-wise cluster correlations (Fig. 5B) and gene net-work analysis (fig. S17) further supported theconclusion that PV-like, SST, and HTR3A inter-neuron classes are conserved in reptiles andmammals. [Note that transcriptomics identifiesVIP- and PV-like interneurons even though VIPand PVALB are not reliably expressed in thesecells (Fig. 5A).]

In turtle and lizard, markers of MGE- and CGE-derived interneurons were expressed in cells scat-tered throughout the pallium, including the dorsalcortex (Fig. 5C). As in mammals, where MGE-and CGE-derived interneurons have differentdensities across cortical layers, neurons express-ing ADARB2 (HTR3A) and SST (SST) were foundpreferentially in superficial and deep dorsalcortex, respectively; NDNF (HTR3A Reln) wasexpressed in rare dorsal cortex subpial cells,reminiscent of mammalian L1 neurogliaformcells (Fig. 5, D and E). Because the same classesof cortical GABAergic neurons exist in mammalsand reptiles, they likely existed in their amnioteancestor. Our analysis did not detect similaritiesat a finer level: For example, we found no turtle

Tosches et al., Science 360, 881–888 (2018) 25 May 2018 5 of 8

DM L

V

A

C

B

Habib et al 2016

DG

CA

3C

A1

Meis2Ndrg1Bhlhe41Bhlhe40Nr4a2Egr1Nr2f2Man1aSox5Bcl11aCnr1Lmo4Slit2Plxna1Cpne7Etv1Arhgef6Cplx1Coch **Wscd1Homer3BokCnih3Lrrtm4Kcng1Kcnip4Zfp536Bcl11bMef2cPenkProx1Lmo3

Expression(Z-score)

maxmin

e29

e30

e31

e32

e33

e34

e35

e37

e38

e36

MEIS2NDRG1BHLHE41BHLHE40NR4A2EGR1NR2F2MAN1A1SOX5BCL11ACNR1LMO4SLIT2PLXNA1CPNE7ETV1ARHGEF6CPLX1COCHWSCD1HOMER3BOKCNIH3LRRTM4KCNG1KCNIP4ZNF536BCL11BMEF2CPENKPROX1LMO3

MC DMC

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e29

e30

e31

e32

e33

e34

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0

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0.55

0

Correlatione01e02e03

e09e10

e06e07

e04e05

e29

e30

e31

e32

e33

e34

e35

e37

e38

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DG

CA3

CA1

PROX1 ETV1 SOX5COCHZBTB20

DMC

MC

Fig. 3. Molecular architecture of the reptilian hippocampus. (A)Expression of hippocampal markers in turtle medial (MC) and dorsomedial(DMC) cortices. Arrowheads indicate boundaries between DG, CA3, andCA1 (compare to schematic at right). D, dorsal; V, ventral; M, medial; L,lateral. (B) Pairwise correlations of turtle and lizard (top) and turtle andmouse (bottom) hippocampal clusters. Dots indicate statistically signifi-

cant correlations. In lizard, the ZBTB20+ ETV1+ medial cortices aretermed DMC and D1 in the classical literature but correspond to turtleDMC. (C) On the left, expression of mammalian hippocampal markers inturtle single cells (columns, arranged by cluster) and, on the right,expression of the same markers in mouse [data from (19)]. Transcriptionfactor names are in red. Scale bars, 200 mm.

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clusters corresponding to mammalian Martinottior basket cells. This suggests that species-specificsubtypes of interneuronsdiversified independentlyin mammals and reptiles from ancestral PV-like,SST, and HTR3A (possibly VIP-like and Reln) cellclasses.

Discussion

Our single-cell data provide molecular supportto the existence of conserved regions and celltypes in the amniote pallium. Homologs of themammalian neocortex, “core” hippocampus (withdentate and CA fields), claustrum, and pallialamygdala probably existed already in stem am-niotes. Glutamatergic neurons with an UL- orDL-like genetic signature exist in turtle anterior

dorsal cortex, but one-to-one homologies of thesecell types and individual mammalian layer typesare not supported by our data. By contrast, cor-tical GABAergic interneuron classes (SST, PV-like, and HTR3A) are ancestral in amniotes.Our analysis indicates that mammalian and

reptilian brains diversified by expansion and in-dependent evolution of different pallial territo-ries and that these expansions coincided withthe evolution of new neuronal types. The largereptilian anterior DVR (ventral pallium), forexample, consists of spatially segregated neuro-nal types specialized in processing visual, audi-tory, or somatosensory stimuli (17). The samesensory pathways also reach the ventral palliumof mammals (for example, the lateral amygdala)

but are not processed by dedicated neuronal pop-ulations there (12). This suggests that the elab-oration of DVR neurons and circuits is specificto reptiles and birds.The situation is reversed with the dorsal pal-

lium. Mammalian neocortex emerged by expan-sion of a small dorsal pallial territory, homologousto the anterior dorsal cortex of reptiles and tothe avian Wulst (1). This may have coincidedwith the generation of new glutamatergic celltypes from the diversification of UL- and DL-likeneurons. The sequential generation of neuronswith distinct identities is a conserved feature ofmammalian and reptilian (33) dorsal palliumprogenitors, and corticothalamic neurons areearly born neurons in mouse and turtle (28).

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mouse UL specific or enriched markers mouse DL specific or enriched markers

WFS1

RASGRF2

GUCY1A3

RFX3LH

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NEUROD6

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NR2F1

ETV1TCERG1L

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SOX5

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0.0

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A

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L5b Chrna6L5b Tph2L5b Cdh13

L6a Car12L6a Syt17L6a MgpL6a Sla

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Correlation

UL-like

turtle

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DL-like

UL

DL

DM L

V

aDC

SATB2

SOX5

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Fig. 4. UL- and DL-like neurons in turtle dorsal cortex. (A) Dot-plotshowing expression of canonical mammalian layer markers (columns) in turtleanterior dorsal cortex (aDC) clusters (rows). Dot size indicates the percentageof cells in the cluster where the gene is detected; color indicates expression(exp) level. Names of transcription factors are in red. (B) ISHs showingexpression of mammalian UL and DL transcription factors throughout the turtleaDC. Arrowheads indicate the medial and lateral boundaries of anterior dorsalcortex. Scale bar, 500 mm. (C) Pairwise correlations of turtle aDC (columns) and

mouse neocortex (rows) glutamatergic types. Dots indicate statisticallysignificant correlations. Mouse clusters are from (7). (D) Left panel, turtle DL-likecells, labeled by PTHLH (green), are preferentially found in superficial L2 [blue,4ʹ, 6-diamidino-2-phenylindole (DAPI)]. Middle panel, double ISH for SATB1(enriched inUL-like cells,magenta) and ETV1 (e07DL-like cells, green), showingthe relative positions of these cells. Right panel, schematic summarizing thedistribution of UL- and DL-like glutamatergic neurons (inverse arrangement tothat observed in mammals). See also fig. S15. Scale bar, 100 mm.

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Neuronal birth order is the same in turtle andmammals (DL first, UL late) (28), and the super-ficial position of turtle DL-like neurons is consist-entwith the inversion of corticogenesis (outside-inin reptiles, inside-out in mammals) (28, 34). Fi-nally, inmammals, transcription factors specify-ingULandDL fate are coexpressed in progenitorsand acquire mutually exclusive expression onlyafter cell-cycle exit (35). The coexpression ofmammalian UL and DL fate specifiers in turtleneurons suggests that cortical layers may have

evolved from the remodeling of regulatory inter-actions between these transcription factors, possi-bly through new repressive interactions. Thetemporal extension of neurogenesis (33) couldhave enabled the segregation of originally over-lapping gene expression programs and thus thediversification of ancestral UL and DL types.These molecular maps of turtle and lizard pal-

lium provide a framework for future functionalstudies. How do similarities and differences ingene expression programs inform us about the

evolution of brain function? Much of reptiliancortex, for example, is molecularly related to coremammalian hippocampus. Lesion experimentsin reptiles suggest a role for medial cortex in navi-gation (22), but no chronic electrophysiologicaldata have, as of yet, been obtained from theseregions. Integrating our molecular maps withtracing, electron microscopy, and electrophysio-logical studies is needed to understand whetherand how gene expression programs are linkedto the evolution of connectivity and function.Common principles of synaptic organization

can be extrapolated from the comparison of three-and six-layered cortices (36). Are these similar-ities coincidental or do they reflect ancestralcortical circuits? In mammals, local circuit motifsinvolve GABAergic types with distinct molecularand functional features (30). Our study indicatesthat interneuron diversity is ancestral to bothmammals and reptiles. The conservation of in-terneuron classes over at least 320 million yearssuggests not only that there is selective pressurefor interneuron diversity but also that interneu-ron diversity itself may have evolved in stemvertebrates within primordial cortical circuits(37). Alternatively, the conservation of interneu-ron classes may result simply from developmentalconstraints on subpallium patterning. The com-bined molecular and functional investigation ofcircuit motifs in reptilian cortex may shed lighton the ancestral design and computational logicof vertebrate cortices.

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ADARB2

L1

L3

L2

LHX6

L1

L3

L2

SST

L1

L3

L2

PLAU

L1

L3

L2

RELN

L1

L3L2

NDNF

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L3L2

ADARB2 + SST

PLAU + SST

LHX6 + SST

ELAVL2

i14

i15

i16

i17

i18

i07

i08

i09

i10

i12

i11

i13

Pvalb Obox3Pvalb Wt1Pvalb Rspo2Pvalb Tacr3Pvalb Cpne5Pvalb TpbgPvalb Gpx3

Sst Tacstd2Sst Cdk6Sst Myh8Sst ThSst ChodlSst Cbln4

IgtpSmad3Ndnf Cxcl14Ndnf Car4

ScngVip Gpc3Vip ChatVip ScngVip Parm1Vip Mybpc1

SS

TP

VV

IPR

eln

CGE-derived

turtle

MGE-derived

CG

E-d

eriv

edM

GE

-der

ived

mo

use

(T

asic

et a

l. 2

016)

Correlation

−0.26 0.40

i02

i03

i04

i05

i06

i01

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i16

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i18

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i08

i09

i10

i12

i11

i13

SALL3PAX6ZIC1THZFHX4FOXP2FOXP1SIX3TSHZ1PBX3MEIS2TRHVIPSP8GRPNFIXPROX1NR2E1HTR3AZBTB16SALL1CNR1ADARB2NPAS1NPY1RNR2F2SLC1A2LRRTM4PENKTNFAIP8L3RGS12NDNFID2RELNZEB2DLX1CALB1CBLN4ELFN1EFNA5CTNND2CACNG3HTR1ANPYSSTSATB1BCL11AARXLHX6SOX6ENO2KCNC2KCNC1S100A1BTBD3TRPS1CNTNAP4GABRB2LMO3BCANETV1PVALBPLAU

Vip

Rel

nS

ST

PV

VipSp8GrpNfixProx1Nr2e1Htr3aZbtb16Sall1Cnr1Adarb2Npas1Npy1rNr2f2Slc1a2Lrrtm4PenkTnfaip8l3Rgs12Ndnf**Id2RelnZeb2Dlx1Calb1Cbln4Elfn1Efna5Ctnnd2Cacng3

NpyHtr1a

SstSatb1Bcl11aArxLhx6Sox6Eno2Kcnc2Kcnc1S100a1Btbd3Trps1Cntnap4Gabrb2Lmo3BcanEtv1PvalbPlau

Tasic et al.2016

Expression(Z-score)

maxmin

striatum amygdala OB

septum LGE-derived

SST PV-likeHTR3AVIP-like

HTR3AReln

CGE-derived MGE-derivedA

B C

E

D

SST PV-likeVIP-like Reln

Fig. 5. Turtle GABAergic interneurons.(A) On left, heatmap showing expression ofselected mammalian GABAergic markers(rows) in turtle single cells, grouped bycluster (column), and, on right, expressionof the same markers in mouse corticalGABAergic cells [data from (7)]. Names oftranscription factors are in red. OB, olfactorybulb. (B) Pairwise correlations of turtle(columns) and mouse (rows) MGE- andCGE-derived GABAergic clusters. Dotsindicate statistically significant correlations.(C) GABAergic neurons, labeled by ELAVL2, inturtle. (D) Double labeling of SST (immuno-histochemistry, magenta) and ADARB2,PLAU, or LHX6 (ISH, green) in turtle dorsalcortex. LHX6 labels both SST+ (SST) andSST– (PV-like) neurons. White arrowheadsindicate SST neurons (SST+ LHX6+); bluearrowheads indicate PV-like neurons(PLAU+ LHX6+ SST−); green arrowheadsindicate HTR3A neurons (ADARB2+).Scale bars, 20 mm. (E) ISHs of GABAergicmarkers in turtle dorsal cortex.

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ACKNOWLEDGMENTS

The authors are grateful to V. Benes and P. Collier (EMBL GeneCoreFacility, Heidelberg) for training and support on sequencing;A. Georges (University of Canberra) for prepublication access tothe Pogona genome; C. Müller (MPI for Brain Research) forinitial investigations on turtle GABAergic interneurons; M. Klinkmann,A. Arends, A. Macias Pardo, T. Manthey, C. Thum, and J. Knopfor technical assistance; S. Masneri for help with scientific computing;and E. Schuman, C. Müller, S. Reiter, and the Laurent laboratoryfor feedback during the course of this work and on the manuscript.

Funding: This research was funded by the Max Planck Societyand the European Research Council under the European Union’sSeventh Framework Programme (FP7/2007-2013)/ERC grantagreement n° 322705 (G.L.). Author contributions: Single-cellexperiments: M.A.T. and T.M.Y.; bioinformatics: M.A.T., T.M.Y.,and G.T.; anatomy and histology: M.A.T., R.K.N., and A.A.J.; dataanalysis: M.A.T., T.M.Y., R.K.N., A.A.J., G.T., and G.L.; projectmanagement and supervision: G.L.; and manuscript writing:M.A.T. and G.L., with input from T.M.Y. and R.K.N. Competinginterests: The authors declare no competing interests. Data andmaterials availability: Sequencing data have been deposited inthe NCBI Sequence Read Archive (BioProject PRJNA408230),and processed gene expression data can be explored at https://brain.mpg.de/research/laurent-department/software-techniques.html. The code used for analysis is available at https://github.molgen.mpg.de/MPIBR/ReptilePallium/.

SUPPLEMENTARY MATERIALS

www.sciencemag.org/content/360/6391/881/suppl/DC1Materials and MethodsFigs. S1 to S17Tables S1 and S2References (38–55)

6 November 2017; accepted 12 March 2018Published online 3 May 201810.1126/science.aar4237

Tosches et al., Science 360, 881–888 (2018) 25 May 2018 8 of 8

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Page 9: Evolution of pallium, hippocampus, and cortical cell types … · Fig. 1E and Fig. 2B), in agreement with higher-level clustering analysis and with our tissue dis-sections (figs

transcriptomics in reptilesEvolution of pallium, hippocampus, and cortical cell types revealed by single-cell

Maria Antonietta Tosches, Tracy M. Yamawaki, Robert K. Naumann, Ariel A. Jacobi, Georgi Tushev and Gilles Laurent

originally published online May 3, 2018DOI: 10.1126/science.aar4237 (6391), 881-888.360Science 

, this issue p. 881Sciencerepresented as adjacent fields in the reptile brains.evolutionary span, although subtypes were species-specific. Pieces of the much-folded mammalian hippocampus wereadult neural stem cells shared evolutionary origins. General classes of interneuron types were represented across the from the reptilian three-layered cortex. Despite a lack of correspondence between layers, mammalian astrocytes andturtle, lizard, mouse, and human brain samples. They assessed how the mammalian six-layered cortex might be derived

used single-cell transcriptomics to studyet al.Just how related are reptilian and mammalian brains? Tosches Evolution of the brain

ARTICLE TOOLS http://science.sciencemag.org/content/360/6391/881

MATERIALSSUPPLEMENTARY http://science.sciencemag.org/content/suppl/2018/05/02/science.aar4237.DC1

REFERENCES

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