Kiwi genome provides insights into evolution of a nocturnal lifestyle

Table 2 Annotated opsins in the Apteryx mantelli genome

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 Glu^3.49Lys	0.02093	0.26785	44.951*
augustus_masked-scaffold1068-abinit-gene-0.2-mRNA-1	OPN1SW†	Partial sequence, deleterious mutation Glu^6.30Gly	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

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.
*P value <0.05
†Tested on orthologs in Tinamus guttatus, Antrostomus carolinensis, Taeniopygia guttata, Gallus gallus, and Apteryx mantelli (not present in Struthio camelus and Tyto alba assemblies)
††Tested on orthologs in Chlamydera nuchalis, Chlamydera maculata, Sericulus chrysocephalus, Ptilonorhynchus violaceus, Scenopoeetes dentirostris, Ailuroedus crassirostris, Falco cherrug, Columba livia, and Apteryx mantelli

ISSN: 1474-760X