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. 2009 Jun 10;29(23):7519–7525. doi: 10.1523/JNEUROSCI.0517-09.2009

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Copyright © 2009 Society for Neuroscience 0270-6474/09/297519-07$15.00/0

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Figure 4. — Phylogenetic analysis of P. regius and X. unicolor LWS, SWS1, and Rh1 retinal opsins (GenBank accession numbers FJ497233-FJ497238) with LWS, SWS1, SWS2, RhB/Rh2, and RhA/Rh1 visual pigment coding sequences of other vertebrate species. Posterior probability values (represented as a percentage) are indicated for each resolved node. The scale bar indicates the number of nucleotide substitutions per site. The ciliary opsin of Dumeril's clam worm, Platynereis dumerilii, was used as an outgroup (data not shown). The sequences used for generating the tree are as follows: (1) RhA/Rh1 opsin class: human (Homo sapiens), NM000539; fat-tailed dunnart (Sminthopsis crassicaudata), AY159786; platypus (Ornithorhynchus anatinus), EF050076; pigeon (Columba livia), AH007730; sunbeam snake (Xenopeltis unicolor), FJ497233; python (Python regius), FJ497236; green anole (Anolis carolinensis), AOIRHODOPS; clawed frog (Xenopus laevis), NM001087048; Comoran coelacanth (Latimeria chalumnae), AF131253; Australian lungfish (Neoceratodus forsteri), EF526295; zebrafish (Danio rerio), NM131084; little skate (Raja erinacea), U81514; pouched lamprey (Geotria australis) (RhA), AY366493; (2) RhB/Rh2 opsin class: pigeon (Columba livia), AH007731; green anole (Anolis carolinensis), AH004781; Australian lungfish (Neoceratodus forsteri), EF526296; Comoran coelacanth (Latimeria chalumnae), AF131258; zebrafish (Danio rerio), NM131253 (Rh2.1); pouched lamprey (Geotria australis) (RhB), AY366494; (3) SWS2 opsin class; platypus (Ornithorhynchus anatinus), EF050077; pigeon (Columba livia), AH007799; green anole (Anolis carolinensis), AF133907; clawed frog (Xenopus laevis), BC080123; Australian lungfish (Neoceratodus forsteri), EF526299; zebrafish (Danio rerio), NM131192; pouched lamprey (Geotria australis), AY366492; (4) SWS1 opsin class: human (Homo sapiens), NM001708; fat-tailed dunnart (Sminthopsis crassicaudata), AY442173; pigeon (Columba livia), AH007798; sunbeam snake (Xenopeltis unicolor), FJ497234; python (Python regius), FJ497237; green anole (Anolis carolinensis), AH007736; Australian lungfish (Neoceratodus forsteri), EF526298; clawed frog (Xenopus laevis), XLU23463; pouched lamprey (Geotria australis), AY366495; zebrafish (Danio rerio), NM131319; (5) LWS opsin class: human (Homo sapiens), NM020061; fat-tailed dunnart (Sminthopsis crassicaudata), AY430816; platypus (Ornithorhynchus anatinus), EF050078; sunbeam snake (Xenopeltis unicolor), FJ497235; python (Python regius), FJ497238; green anole (Anolis carolinensis), ACU08131; clawed frog (Xenopus laevis), XLU90895; Australian lungfish (Neoceratodus forsteri), EF526297; zebrafish (Danio rerio), NM131175; pigeon (Columba livia), AH007800; pouched lamprey (Geotria australis), AY366491.