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Appendix 4-figure 9A Opsin gene tree

posted on 2018-08-13, 17:32 authored by Timothy FallonTimothy Fallon
Opsin Maximum likelihood (ML) tree. Collected opsin sequences were multiple sequence aligned with MAFFT L-INS-i[163] with default parameters. Gaps and ambiguous sequences were filtered with trimAL software[304] (parameter: -gt =0.5), and the ML tree reconstructed with MEGA7[252] with LG+G (5 gamma categories (+G, parameter = 1.3856) substitution model using 362 aa of multiple amino acid alignment. 100 bootstrap replicates were performed. HsapGPR was used as the outgroup sequence. Black circles on each node indicate bootstrap values. Scale bar equals substitutions per site. Taxon abbreviation: Hsap: Homo sapiens, Mnem: Mnemiopsis leidyi Agam: Anopheles gambiae, Sfre: Sympetrum frequens, Ilum: Ignelater luminosus, Bmor: Bombyx mori, Ppyr: Photinus pyralis, Tcas: Tribolium castaneum, Dmel: Drosophila melanogaster.