JCoDA: a tool for detecting evolutionary selection

BMC Bioinformatics

Table 1 Analysis of sex determination pathway genes

Gene	Pathway	dN/dS	M7-vs-M8	Proportion of sites with dN/dS>1
fem-1	B	0.13	0.86	0.7
fem-2	B	0.12	3.49	2.6
fem-3	B	0.27	0.99	3.8
her-1	B	0.19	0.09	0.6
laf-1	B	0.04	2.34	1.1
tra-1	B	0.25	7.93	6.0
tra-2	B	0.29	1.60	0.0
fox-1	S	0.06	0.02	0.7
sdc-1	S	0.24	0.72	0.0
sdc-2	S	0.35	3.30	0.0
sdc-3	S	0.45	7.21	7.8
sea-1	S	0.57	11.44	52.5
sea-2	S	0.32	20.11	21.7
sel-10	S	0.06	8.21	1.7
sex-1	S	0.22	12.47	1.6
xol-1	S	0.32	2.66	0.0
fbf-1/2*	G	0.15	3.93	1.3
fog-1	G	0.17	12.30	4.5
fog-2*	G	0.51	48.23	19.2
fog-3	G	0.18	0.67	2.0
gld-1	G	0.07	7.17	1.6
gld-3	G	0.35	36.55	10.9
mog-1	G	0.02	4.87	0.4
mog-6	G	0.04	1.09	0.2
nos-3	G	0.39	50.41	22.5

Genes are sorted based on functions in germ line and somatic sex determination (B), somatic sex determination (dosage compensation) (S), or germ line sex determination (G). All sex determination gene orthologs used were identified by reciprocal best-hit or conserved synteny (Wormbase). Only genes with large indels and obvious mispredictions that could be resolved were eliminated. dN/dS = average pairwise score for the gene family (Nei & Gojobori, 1986). Models compared for likelihood ratio test (LRT) were M7(dN/dS>1 disallowed, null) -vs- M8(dN/dS>1 allowed, alternate), where bold indicates number higher than critical value (Df = 2, χ²_l = 5.9915, p = 0.05) and rejection of the null. Portion of sites with dN/dS>1 was calculated as a ratio of selected sites with a probability higher than 0.5 of dN/dS>1 to total sites. Tree files were based on the ClustalW alignments using the neighbor-joining method (Phylip). See associated FASTA files for ID numbers and species used. (*) = species specific gene expansion or contains species specific duplications.

ISSN: 1471-2105