Table 1.

Number of postulated gain/loss events in comparing S. mansoni genes with those present in nematodes, arthropods and deuterostomes

	Cases*				# of genes	# of Loss/Gain events under each theory
	Sm	Nem	Arthr	Deut		APC	LED
Group 1	1	1	1	1	4,244	0	0
Group 2	1	0	0	1	427	2 × 427 = 854	1 × 427 = 427
Group 3	1	0	1	0	436	2 × 436 = 872	2 × 436 = 872
Group 4	1	1	0	0	61	1 × 61 = 61	2 × 61 = 122
Group 5	1	1	1	0	289	1 × 289 = 289	1 × 289 = 289
Group 6	1	0	1	1	998	1 × 998 = 998	1 × 998 = 998
Group 7	1	1	0	1	49	1 × 49 = 49	1 × 49 = 49
TOTAL					6,504	3,123	2,757
Excess losses/gains (APC – LED)						366
Significance (p-value)**						2.2 × 10-16

* S. mansoni (Sm) genes were compared to genes from all organisms of the following clades: Nematodes (Nem), Arthropods (Arthr) and Deuterostomes (Deut). Each group represents one of the possible cases: when S. mansoni genes were present in at least one organism of the indicated clade it was marked with 1; when genes were absent from all organism of that clade it was marked with 0. For example, group 1 represents the case where 4,244 S. mansoni genes were present in all three clades studied, and therefore no loss/gain events were computed; similarly, group 2, represents the case where 427 S. mansoni genes were not present in Nematodes or Arthropods, and under the APC hypothesis two loss/gain events per gene were computed, whereas under the LED hypothesis only one event per gene was counted. A schematic representation of these cases and the minimal number of events required under either of the two hypotheses is shown in Additional file 1. ** P-value was calculated using 100,000 bootstrapped samples followed by Wilcoxon Test.