Table 7.

Comparison of results from the different phylogenetic analyses

	Nc/Gm	C/Gm	C/Gb
(A) Comparison of variable and informative characters and g1 statistic value among data matrices with different treatments of ambiguous regions and gaps
Variable characters	126	121	131
Informative characters	15	17	17
g1	−0·4514	−0·49669	−0·4484

		MP
Clade	NJ % bootstrap	Nc/Gm/Uw % bootstrap	C/Gm/Uw % bootstrap	C/Gb/Uw % bootstrap	Nc/Gm/W % bootstrap	C/Gm/W % bootstrap	C/Gb/W % bootstrap
(B) Tree scores and bootstrap values (%) of clades obtained from different phylogenetic reconstruction methods
1	95	62	59	67	64	69	73
2	94	25	35	38	34	41	54
3	44	77	74	78	87	88	81
4	46	59	62	60	98	100	100
MPTs	–	3	3	3	3	3	2
Tree length	–	145	188	199	130·5	170·5	181·5
CI	–	0·945	0·9521	0·955	0·994	0·996	0·996
RI	–	0·556	0·55	0·55	0·912	0·921	0·921
RC	–	0·525	0·524	0·525	0·907	0·917	0·917
HI	–	0·055	0·0479	0·045	0·006	0·004	0·004

NJ, neighbour joining; MP, maximum parsimony; Nc, ambiguous region not coded; C, ambiguous region coded; Gm, gaps treated as missing data; Gb, gaps treated as fifth base; Uw, characters specified as unweighted; W, characters specified as weighted.

In the clade column the numbers are the different clades of the trees: 1, H. rosmarinifolium–H. linifolium clade; 2, Spanish Haplophyllum clade; 3, H. blanchei–H. coronatum clade; 4, H. rosmarinifolium–H. linifolium–H. bastetanum–H. blanchei–H. coronatum clade.

MPTs, number of most parsimonious trees; CI, consistency index; RI, retention index; RC, rescaled consistency index; HI, homoplasy index.

Bootstrap values <50 %, which appear only in the original NJ tree and in the bootstrap-consensus tree including groups compatible with 50 % majority-rule consensus, are printed in bold.