Fig. 6: Within-species allelic imbalance corresponds to between-species transcriptional divergence.

a Testes from C57BL/6, CAST/EiJ and CAROLI/EiJ mice were subjected to 10x Genomics scRNA-Seq in duplicates. The mouse and testis icons were created with Biorender.com. b Sperm differentiation was highly conserved among all three mice, with similar differentiation trajectories and cell type distributions. The UMAPs display 6098 (B6), 5080 (CAST) and 11,380 (CAROLI) cells respectively. c Legend showing the representation of sub cell types by colours. Hierarchical clustering of dynamic differential expression trajectories for CAST / B6 and CAROLI / B6 (d and e, respectively). Left: Proportion of genes assigned to each cluster. Right: Average relative expression divergence across pseudotime for genes assigned to the four clusters peaking late in differentiation. Bottom: Average effect size for all genes with dynamic differential expression across differentiation irrespective of cluster membership. n specifies the number of genes. Trajectories are derived by LOESS-smoothing, shown with 95% confidence intervals. f Correlation-based measure of expression divergence. Shown are the average correlation coefficients between pairs of B6 versus B6 cells, B6 vs CAST and B6 vs CAROLI cells. Whiskers represent top- and bottom 10% quantiles. Bottom: Difference between average B6-B6 and B6-CAST/B6-CAROLI correlations. The smoothing line is estimated by loess-regression and shown with 95% confidence intervals.