A

All brain nuclei clustered

<figure><img src="image_63.png" /></figure>

B

nompC (AAEL019818)

<figure><img src="image_64.png" /></figure>

C

Pdf (AAEL001754)

<figure><img src="image_65.png" /></figure>

D

Clock cell gene percentage

<figure><img src="image_66.png" /></figure>

E

Fly-mosquito neurons

<figure><img src="image_67.png" /></figure>

F

Fly-mosquito glia

<figure><img src="image_68.png" /></figure>

G

Fly glia-mosquito neurons

<figure><img src="image_69.png" /></figure>

H

<figure><img src="image_70.png" /></figure>

I

Mosquito brain clusters

<figure><img src="image_71.png" /></figure>

J

Mosquito brain clusters

<figure><img src="image_72.png" /></figure>

K

<figure><img src="image_73.png" /></figure>

L

Hr51 (AAEL020847)

MsNPF (AAEL019691)

N Imp1 (AAEL006876)

O mamo (AAEL019481)

P pde8 (AAEL019528)

<figure><img src="image_74.png" /></figure>
**Figure S9. SAMap analysis and identification of clock cells and Kenyon cells, related to Figure 6**

(A) UMAP of brain nuclei clustered using the Leiden algorithm (resolution = 5).

(B and C) Normalized expression of *nompC* (B) and *Pdf* (AAEL001754) (C). Normalized expression is $\ln([([\text{raw count}/\text{total cell counts}] \times \text{median total counts across cells}] + 1))$.

(D) Fraction of total transcripts per cell of 10 putative clock cell gene markers (Table S1). Cluster with high expression highlighted in gray box, enlarged in inset.

(E–G) UMAP of manifold integration of snRNA-seq data from *Aedes aegypti* mosquito brain and published *Drosophila melanogaster* fly head.¹⁸ Plots show integration of fly neurons with mosquito neurons (E), fly glia with mosquito glia (F), and, as a control, fly glia with mosquito neuron (G). Alignment scores are 0.64, 0.64, and 0.47, respectively.

(H–J) Correlation matrices of mapping scores between *Drosophila melanogaster* head annotations and *Aedes aegypti* of clusters (Leiden, resolution = 5) for neuronal cell types (H), glial cell types (I), and Kenyon cell subtypes (J). For all numerical values, see Table S3.

(K) Volcano plot of DEGs between male and female cells in the SVP glia (AAEL002765) cluster. Significant genes (red) had |log fold change| > 1, false discovery rate < 0.05, determined by MAST on normalized expression (Table S2). Male-biased genes are on the right, indicated by Nix (AAEL022912).

(L–P) Normalized gene expression of *Hr51* (AAEL020847) (L), *sNPF* (AAEL019691) (M), *Imp1* (AAEL006876) (N), *mamo* (AAEL019481) (O), *Pde8* (AAEL019528) (P).