Table 1.

87 taxa included in this study

Clade	Species	Acc. #	Tissue #	Voucher Museum #	Study
Esociformes	Esox lucius	AP004103			Ishiguro et al. 2003 [43]
	Dallia pectoralis	AP004102			Ishiguro et al. 2003 [43]
Salmoniformes	Coregonus lavaretus	AB034824			Miya & Nishida 2000 [44]
	Thymallus thymallus	FJ853655			Yasuike et al. 2010
	Salvelinus alpinus	AF154851			Doiron et al. 2002
Argentiniformes	Bathylagus ochotensis	AP004101			Ishiguro et al. 2003 [43]
	Nansenia ardesiaca	AP004106			Ishiguro et al. 2003 [43]
	Glossanodon semifasciatus	AP004105			Ishiguro et al. 2003 [43]
	Opistophroctus soleatus	AP004110			Ishiguro et al. 2003 [43]
Osmeriformes	Retropinna retropinna	AP004108			Ishiguro et al. 2003 [43]
	Salangichthys microdon	AP004109			Ishiguro et al. 2003 [43]
	Mallotus villosus	HM106491			Li et al. 2010
	Plecoglossus altivelis	AB047553			Ishiguro et al. 2001
Stomiiformes	Diplophos taenia	AB034825			Miya & Nishida 2000 [44]
	Chauliodus sloani	AP002915			Miya et al. 2001 [33]
	Gonostoma gracile	AB016274			Miya & Nishida 1999 [45]
Galaxiiformes	Galaxiella nigrostriata	AP006853			Miya et al. (unpubl.)
	Galaxias maculates	AP004104			Ishiguro et al. 2003 [43]
	Galaxias gollumoides	HM106487			Li et al. 2010
Aulopiformes	Synodus variegatus	AY524977			Chen & Wu (unpubl.)
	Chlorophthalmus agassizi	AP002918			Miya et al. 2001 [33]
	Aulopus japonicus	AB047821			Kawaguchi et al. 2001 [33]
	Harpadon microchir	AP002919			Miya et al. 2001 [33]
	Saurida undosquamis	AP002920			Miya et al. 2001 [33]
Ateleopodiformes	Ateleopus japonicus	AP002916			Miya et al. 2001 [33]
	Ijimaia dofleini	AP002917			Miya et al. 2001 [33]
Lampriformes	Lampris guttatus	AP002924			Miya et al. 2001 [33]
	Zu cristatus	AP002926			Miya et al. 2001 [33]
	Trachipterus trachypterus	AP002925			Miya et al. 2001 [33]
Myctophiformes	Neoscopelus macrolepidotus	AP012238	KU 3297	Uncatalogued	This study
	Neoscopelus microchir	AP002921			Miya et al. 2001 [33]
	Scopelengys tristis	AP012228	NSMT-P 99997	NSMT-P 99997	This study
	Solivomer arenidens	AP012249	NSMT	Uncatalogued	This study
	Benthosema fibulatum	AP012253	NSMT-P 75816	NSMT-P 75816	This study
	Benthosema glaciale	AP012264	ZMUC #8160	ZMUC P2393965	This study
	Benthosema pterotum	AP012260	NSMT-P 75855	NSMT-P 75855	This study
	Bolinichthys distofax	AP012232	NSMT-P 97624	NSMT-P 97624	This study
	Bolinichthys pyrsobolus	AP012261	NSMT-P 92273	NSMT-P 92273	This study
	Centrobranchus choerocephalus	AP012237	NSMT-P 102902	NSMT-P 102902	This study
	Ceratoscopelus maderensis	AP012259	ZMUC #6600	ZMUC P2393929	This study
	Diaphus chrysorhynchus	AP012230	NSMT-P 79902	NSMT-P 79902	This study
	Diaphus gigas	AP012235	NSMT-P 91530	NSMT-P 91530	This study
	Diaphus luetkeni	AP012231	ASIZP 911514	ASIZP66276	This study
	Diaphus splendidus	AP002923			Miya et al. 2001 [33]
	Diaphus theta	AP012240	KU 2135	KU 27971	This study
	Diogenichthys atlanticus	AP012233	SIO 09320	SIO 09320	This study
	Electrona antarctica	AP012248	ZMUC #7552	ZMUC P2393962	This study
	Gymnoscopelus nicholsi	AP012250	ZMUC #7806	ZMUC P2393963	This study
	Krefftichthys anderssoni	AP012236	ZMUC #7550	ZMUC P2393964	This study
	Lampadena anomala	AP012227	ME 4201#3	ZMUB 18019	This study
	Lampadena urophaos atlantica	AP012251	ME 7371#4	ZMUB 18050	This study
	Lampadena yaquinae	AP012257	NSMT-P 72341	NSMT-P 72341	This study
	Lampanyctus macdonaldi	AP012241	ZMUC #8077	ZMUC P2393967	This study
	Lampanyctus crocodilus	AP012258	ZMUC #8076	ZMUC P2393968	This study
	Lobianchia gemellarii	AP012242	ME 4239#6	ZMUB O.1725	This study
	Myctophum affine	AP002922			Miya et al. 2001 [33]
	Myctophum asperum	AP012234	NSMT-P 91490	NSMT-P 91490	This study
	Myctophum nitidulum	AP012255	NSMT-P 92345	NSMT-P 92345	This study
	Myctophum orientale	AP012254	NSMT-P 77350	NSMT-P 77350	This study
	Myctophum punctatum	AP012239	ZMUC #6594	ZMUC P2393969	This study
	Nannobrachium ritteri	AP012247	KU 2237	KU 28276	This study
	Notoscopelus caudispinosus	AP012256	KU 5301	MCZ 161883	This study
	Notoscopelus japonicus	AP012252	BSKU 103772	BSKU 103772	This study
	Notoscopelus kroyeri	AP012262	ZMUC #8078	ZMUC P2393970	This study
	Notolychnus valdiviae	AP012229	NSMT-P 102930	NSMT-P 102930	This study
	Protomyctophum arcticum	AB648909-10	ZMUC #8476	ZMUC P2393971	This study
	Stenobrachius leucopsarus	AP012245	NSMT-P 78748	NSMT-P 78748	This study
	Symbolophorus californiensis	AP012246	NSMT-P 92257	NSMT-P 92257	This study
	Taaningichthys minimus	AP012244	ME 5633	ZMUB 18049	This study
	Triphoturus nigrescens	AP012243	NSMT-P 102934	NSMT-P 102934	This study
Ophidiiformes	Cataetyx rubrirostris	AP004407			Miya et al. 2003 [46]
	Carapus bermudensis	AP004404			Miya et al. 2003 [46]
	Bassozetus zenkevitchi	AP004405			Miya et al. 2003 [46]
Lophiiformes	Sladenia gardineri	AB282827			Miya et al. 2010 [47]
	Coelophrys brevicaudata	AB282834			Miya et al. 2010 [47]
	Thaumatichthys pagidostomus	AB282847			Miya et al. 2010 [47]
Percopsiformes	Percopsis transmontana	AP002928			Miya et al. 2001 [33]
	Aphredoderus sayanus	AP004403			Miya et al. 2003 [46]
Polymixiiformes	Polymixia japonica	AB034826			Miya & Nishida 2000 [44]
	Polymixia lowei	AP002927			Miya et al. 2001 [33]
Gadiformes	Stylephorus chordatus	AB280688			Miya et al. 2007
	Bregmaceros transmontana	AP004411			Miya et al. 2003 [46]
	Trachyrincus murrayi	AP008990			Satoh et al. 2006 [48]
	Lota lota	AP004412			Miya et al. 2003 [46]
Zeiformes	Zeus faber	AP002941			Miya et al. 2001 [33]
	Parazen pacificus	AP004433			Miya et al. 2003 [46]
	Zenion japonicum	AP004434			Miya et al. 2003 [46]

Taxa included in this study listed according to ordinal classification. Mitogenome accession number, tissue number, specimen + institute number and study noted if information available.