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. Author manuscript; available in PMC: 2015 Jun 1.
Published in final edited form as: Mol Phylogenet Evol. 2012 Apr 20;64(2):342–356. doi: 10.1016/j.ympev.2012.04.009

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
a

Clades labeled in Fig. 5.

b

Non-coding region length was calculated as the number of nucleotides from the 3′ end of tRNATHR to the 5′ end of the goose hairpin.

c

Percent 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.