Table 3.

Gene order, non-coding region length and percent control region differences for parrot species with a duplicated control region.

Taxa	Source	Cladea	Gene order	Non-coding region lengthb	%CR differencesc
Amazona albifrons	NMSU	A	Amazona	141	0.6
Amazona farinosa	AF338821	A	Amazona	158	0
Amazona ochrocephala	NMSU	A	Amazona	127	2.1
Pyrilia caica	NMSU	A	Amazona	155	0
Pyrilia barrabandi	BR/NMSU	A	Amazona	160	6
Pionus chalcopterus	NMSU/AF338817-18	A	Amazona	180	0.2
Triclaria malachitacea	BR	A	Amazona	112	2.5
Deroptyus accipitrinus	BR	B	Variant A	319	4.7
Pionites leucogaster	BR	B	Variant A	325	10.9
Forpus xanthopterygius	BR	C	Amazona	129	0.2
Forpus sclateri	NMSU	C	Amazona	117	5
Poicephalus robustus	NMSU	D	Amazona	129	7.7
Psittacus erithacus	NMSU	D	Amazona	88	10.8
Prioniturus montanus	NMSU	E	Amazona	360	1.9
Chalcopsitta cardinalis	NMSU	F	Amazona	84	7.9
Charmosyna placentis	NMSU	F	Amazona	45	2.7
Eos histrio	NMSU	F	Amazona	84	2.3
Glossopsitta porphyrocephala	NMSU	F	Amazona	68	3.3
Lorius albidinucha	NMSU	F	Amazona	73	3.3
Melopsittacus undulatus	NC009134	F	Amazona	58	4.6
Neopsittacus musschenbroekii	NMSU	F	Amazona	88	3.3
Phigys solitarius	NMSU	F	Amazona	32	2.7
Psitteuteles goldiei	NMSU	F	Amazona	81	2.6
Pseudeos fuscata	NMSU	F	Amazona	71	3.5
Trichoglossus haematodus	NMSU	F	Amazona	86	3.3
Vini australis	NMSU	F	Amazona	58	3.5
Cyclopsitta diophthalma	NMSU	F	Amazona	62	5.1
Psittaculirostris edwardsii	NMSU	F	Amazona	60	5.5

^aClades labeled in Fig. 5.

^bNon-coding region length was calculated as the number of nucleotides from the 3′ end of tRNA^THR to the 5′ end of the goose hairpin.

^cPercent control region differences was calculated as the number of nucleotides that differed between the 2 aligned control regions divided by the total number of overlapping nucleotides multiplied by 100. Differences were only counted if they occurred 3′ of the goose hairpin.