Diversification of defensins and NLRs in Arabidopsis species by different evolutionary mechanisms

Table 5 Significant results of analysis of natural selection with codeml site models and FUBAR as well as recombination breakpoints detected with GARD for groups of DEFL genes

CRP groups^a	Group	LRT M1:M2	P ^b	LRT M7:M8	P ^b	Estimates for M8^c		M8 BEB sites^d	FUBAR positive^e	FUBAR positive partitions^f	FUBAR negative^e	FUBAR negative partitions^f	GARD break points^g
CRP0260	S125	12.03	0.03	12.08	0.04	ω = 4.92	p1 = 0.2	5	4	3	2	2	0 (3)
CRP0340	S43	44.01	0.01	24.85	0.01	ω = 5.42	p1 = 0.22	8	6	6	3	3	0 (1)
CRP0360	S81	16.99	0.01	19.27	0.01	ω = 5.66	p1 = 0.16	3	2	3	3	2	0 (2)
CRP0360	S87	38.60	0.01	44.39	0.01	ω = 5.25	p1 = 0.28	14	4	6	2	2	0 (2)
CRP0560	S14	22.32	0.01	10.52	0.05	ω = 3.25	p1 = 0.53	7	3	3	2	2	0 (4)
CRP0580	S65	7.64	0.03	9.57	0.06	ω = 3.66	p1 = 0.08	2	2	N.A.	3	N.A.	N.E.
CRP0830	S63	9.30	0.10	9.52	0.06	ω = 9.65	p1 = 0.04	3	7	8	3	4	0 (2)
CRP1110	S68	16.57	0.01	16.68	0.01	ω = 5.45	p1 = 0.16	7	5	5	2	4	0 (1)

^aCysteine Rich Peptide groups (CRPs) of defensin and defensin-like genes (DEFLs) as defined for A. thaliana in [29]
^b P-values are corrected for multiple comparisons with the Benjamini-Hochberg procedure employing a False Discovery Rate of 0.10. Values in bold represent significant tests in which ω is inferred to be >1.0
^cω is dN:dS estimated under M8; p1 is the inferred proportion of positively selected sites. Positions under positive selection are provided in Additional file 13: Data 8
^dNumber of codon position under positive selection with M8 inferred with Bayes Empirical Bayes analysis with P > 0.9
^eAccording to the FUBAR procedure this is the number of codon positions under positive or negative selection with P > 0.9
^fResults obtained with FUBAR analysis based on the partitions of all breakpoints detected with GARD regardless of their statistical significance
^gNumber of breakpoints with significant phylogenetic topological incongruence at p ≤ 0.1, between parentheses is the total number of breakpoints detected. N.E. means no evidence for recombination was detected. For such groups a second FUBAR analysis was not performed (N.A.)

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