Journal of Insect Science: Vol. 8 | Article 40

Table 1. Assignment of AmbHLH members into corresponding families

bHLH name	Family	Bootstrap support from various phylogenetic analyses
bHLH name	Family	NJ^a	MP^a	ML^a	NJ^b	MP^b	ML^b
AmAse1	ASCa	100	72	100	66	65	73
AmAse2	ASCa	100	91	83	36	n/m*	85
AmAmos1	Atonal	98	84	94	83	71	50
AmAmos2	Atonal	99	93	94	71	44	57
AmAto	Atonal	94	76	94	97	96	78
AmMistr1	Mist	98	88	92	100	100	71
AmMistr2	Mist	99	79	85	100	100	67
AmFer2	PTFb	73-PTFa	56-PTFa	65-PTFa	89-PTFb	98-PTFb	71-PTFb
AmDm	Myc	46	47	55	97	99	77
AmUSF1	USF	99	94	85	97	96	92
AmUSF2	USF	100	98	68	89	93	85
AmAP4	AP4	29-SRC	35-Figα	n/m	55-AP4	n/m	53-AP4
AmClk2	Clock	79	67	68	80	59	62
AmDys	AHR	34	40	88	100	100	82
AmSim	Sim	n/m	50	n/m	72	92	87
AmStich1	Hey	47	58	n/m	100	100	100
AmSide	H/E(spl)	42	50	100	99	99	97
AmH	H/E(spl)	98	63	66	93	79	64
AmDpn	H/E(spl)	92	n/m	n/m	68	n/m*	61
AmE(spl)1	H/E(spl)	n/m	73	n/m	39	n/m	66
AmE(spl)2	H/E(spl)	n/m	35	n/m	n/m*	n/m*	n/m*
AmE(spl)3	H/E(spl)	n/m	41	n/m	n/m*	34	n/m*

n/m = not monophyletic.
n/m* means that a AmbHLH does not form a monophyletic group with one specific bHLH protein but is in a monophyletic group with other bHLH proteins of the same family.
NJ^a, MP^a and ML^a: bootstrap support from constructing NJ, MP and ML trees of in-group phylogenetic analyses with the 45 domains (the constructed trees not shown).
NJ^b, MP^b and ML^b: bootstrap support from constructing NJ, MP and ML trees of in-group phylogenetic analyses with the 59 fruit fly bHLH proteins (the constructed trees not shown).
Each figure in the table is a bootstrap value supporting assignment of the AmbHLH sequence either into the family listed in the column of “Family” or into another family following the figure after a hyphen.