D. pseudoobscura (SP vs Cytes)

I performed differential expression analysis by comparing cells in the SP cluster with cells in EPS, PS1, PS2, and PS3. I then took the list of genes from this analysis (SP-biased, Cyte-biased, Not Significant) and filtered out the orthologs. The majority of orthologs expressed in the germline were conserved with very few genes moving onto the respective Muller element (Table 1).

Table 1. Number of genes per Muller Element.

Using these conservation classes I wanted to see if there were differences in primary spermatocyte expression (EPS, PS1, PS2, PS3). We can look for enrichment in two ways: (1) we can look at the percent of primary spermatocyte cells expressing genes in each class, (2) we can use contingency tables to test to look for a relationship between expression bias and movement class. If MSCI is driving gene movement, we expect that Muller A (X) and D (Neo-X) will have increased movement off for genes important for spermatogenesis. As a control, Muller E (2) would not show selection.

Primary Spermatocyte Expression

In Figures 1-3 I look at the proportion of primary spermatocyte cells that expressed genes in the different movement classes. The number of genes in the moved_on and moved_off classes are very low (< 10) which makes interpretation difficult. I decided to group genes into “Selection Favor” and “Selection Against” for all statistical analyses. Here I compare the distribution of the prorportion of cells using a Mann-Whitney U test. We see an significant increase in primary spermatocyte expression for genes with “Selection Against” for all three Muller elements.

Muller A

Mann-Whitney U (Favor vs Against): 1.084447531668882e-09

Muller D

Mann-Whitney U (Favor vs Against): 5.792143929899031e-30

Muller E

Mann-Whitney U (Favor vs Against): 4.6786534549032415e-51

Enrichment of Primary Spermatocyte Biased Genes

Next, we looked at contingency tables to test for a relationship between primary spermatocyte biased expression and selection against. Again, cell counts are very low for some combinations (Table 2,4,6) so I combined counts to make statistical analysis possible (Table 3,5,7). Again there is evidence of a enrichment of genes that underwent “Selection Against” for all tested Muller elements. While all Muller elements were significant, Muller D shows a more extreme pattern.