Table 2 PtoD estimates and summary statistics indicating balancing selection for the four genes that included at least one putative TSP

			PtoD (p) value (percentile)				Nucleotide diversity (π)			Tajima’s D			F_st			ß score
Contig- transcript	TSP	Gene function	D. magna vs D. sinensis	D. magna vs D. similis	D. similis	D. sinensis	D. magna	D. similis	D. sinensis	D. magna	D. similis	D. sinensis	D. magna vs D. similis	D. similis vs D. sinensis	D. magna vs D. sinensis	D. magna	D. similis	D. sinensis
000011F-21.35	2,141,058	C1q domain-containing protein	50.7 (0)	50.7 (0)	39.1 (0)	37.6 (0)	***	***	***	*	**	***	***	NS	***	***	***	***
000011F-23.73	2,343,857	Cladoceran-specific protein	12.6 (9)	50.2 (0)	28.6 (0)	12.6 (1)	***	*	NS	**	***	***	***	**	***	***	***	***
000018F-16.99	1,611,159	Alpha subunit of putative Na+/K + ATPase	6.2 (15)	7.2 (14)	4.6 (5)	5.1 (3)	***	***	*	NS	NS	**	NS	*	NS	NS	**	**
000028F-3.33	298,723	Metalloendopeptidase	15.2 (7)	7.6 (13)	3.5 (6)	14.1 (1)	NS	***	***	NS	***	***	**	***	**	***	***	***

Details of the position and gene function for the four genes that included at least one putative TSP are reported. PtoD values (corrected for gene length and its value multiplied by 1000) along with their percentiles (in parenthesis) compared to the empirical PtoD distribution of all genes for each species are given. PtoD values for D. magna are calculated in comparison to both D. sinensis and D. similis (for more details see Table S7). Nucleotide diversity, Tajima’s D, F_st, and ß score were calculated in 5 kb non-overlapping sliding windows and we report here the statistical significance of the comparison of the candidate regions, identified as a 100 kb genomic segment centered on the candidate TSP, with the background level of genetic diversity identified as the 20 longest contigs in the genome. All tests are two-sided Wilcoxon tests. p Values, adjusted for false discovery rates, represent results from tests for elevated nucleotide diversity, Tajima’s D and ß score relative to the background, and for reduced F_st (***<0.001; **<0.01; *<0.05; NS ≥ 0.05).

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