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Table 2 Annotated opsins in the Apteryx mantelli genome

From: Kiwi genome provides insights into evolution of a nocturnal lifestyle

AptMant0 annotation ID External gene ID Description ω background ω Apt. mantelli LRT
augustus_masked-scaffold541-abinit-gene-7.0-mRNA-1 RHO No obvious alteration 0.044 0.14913 6.128*
augustus_masked-scaffold1311-abinit-gene-0.1-mRNA-1 OPN1LW Partial sequence TM7 0.15601 0.59702 1.503
maker-scaffold728-augustus-gene-1.2-mRNA-1 OPN1MW Deleterious mutation Glu3.49Lys 0.02093 0.26785 44.951*
augustus_masked-scaffold1068-abinit-gene-0.2-mRNA-1 OPN1SW Partial sequence, deleterious mutation Glu6.30Gly 0.03815 0.19244 5.162*
augustus_masked-scaffold9587-abinit-gene-0.0-mRNA-1 SWS2†† Partial sequence 0.02045 0.0001 0.514
maker-scaffold19-augustus-gene-28.1-mRNA-1 OPN3 No obvious alteration 0.10965 0.54221 3.211
augustus_masked-scaffold39-abinit-gene-55.0-mRNA-1 OPN4-1 No obvious alteration 0.14205 0.23127 2.733
augustus_masked-scaffold122-abinit-gene-6.0-mRNA-1 OPN4-2 No obvious alteration 0.18597 2.57434 8.194*
maker-scaffold597-augustus-gene-1.2-mRNA-1 OPN5 No obvious alteration 0.07114 0.0001 1.733
augustus_masked-scaffold1987-abinit-gene-3.0-mRNA-1 opsin-VA-like No obvious alteration 0.31735 0.26196 0.035
  1. LRT = likelihood ratio testing with one degree of freedom, between the null model (model = 0) and a model where the kiwi branch differs from other birds: chicken, turkey, zebra finch, chuck-will’s-widow, barn owl, tinamou, and ostrich (model = 2), implemented in CODEML from the PAML package [24]. Extended selection analysis in which nocturnal birds, ostrich, and tinamou are sequentially appointed as foreground branch are presented in Additional file 1: Table S10.
  2. *P value <0.05
  3. †Tested on orthologs in Tinamus guttatus, Antrostomus carolinensis, Taeniopygia guttata, Gallus gallus, and Apteryx mantelli (not present in Struthio camelus and Tyto alba assemblies)
  4. ††Tested on orthologs in Chlamydera nuchalis, Chlamydera maculata, Sericulus chrysocephalus, Ptilonorhynchus violaceus, Scenopoeetes dentirostris, Ailuroedus crassirostris, Falco cherrug, Columba livia, and Apteryx mantelli