Table 1. Species and their GenBank accession numbers used in this study.
| Species | Accession number | Source |
| Opsariichthys group | ||
| Parazacco spilurus | KF971863 | Chang et al. 2016 |
| Candidia barbata | This study | |
| Candidia pingtungensis | KT725246 | Yin et al. 2015 |
| Nipponocypris koreanus | KJ427719 | Chen et al. 2016a |
| Nipponocypris sieboldii | AB218898 | Saitoh et al. 2006 |
| Nipponocypris temminckii | KM213515 | Chen et al. 2016b |
| Zacco acanthogenys | KT290890 | Yin et al. 2015 |
| Zacco platypus | AP012115 | Miya et al. 2015 |
| Opsariichthys acutipinnis | KT725245 | Yin et al. 2015 |
| Opsariichthys bidens | DQ367044 | Wang et al. 2007 |
| Opsariichthys chengtui | KT725244 | Yin et al. 2015 |
| Opsariichthys evolans | This study | |
| Opsariichthys pachycephalus | This study | |
| Opsariichthys uncirostris | AB218897 | Saitoh et al. 2006 |
| Xenocyprididae | ||
| Hemigrammocypris rasborella | AP011422 | Tang et al. 2010 |
| Metzia longinasus | KF955011 | Ma & Luo 2016 |
| Metzia mesembrinum | NC_023797 | Yuan et al. 2016 |
| Metzia formosae | NC_022458 | Lin et al. 2015 |
| Metzia lineata | NC_031541 | GenBank |
| Aphyocypris chinensis | AB218688 | Saitoh et al. 2006 |
| Aphyocypris kikuchii | JX184925 | Jang-Liaw et al. 2013b |
| Yaoshanicus arcus | AP011398 | Tang et al. 2010 |
| Nicholsicypris normalis | AP011396 | Tang et al. 2010 |
| Pararasbora moltrechti | JX311312 | Jang-Liaw et al. 2013a |
| Macrochirichthys macrochirus | NC_015551 | GenBank |
| Paralaubuca typus | AP011211 | Saitoh et al. 2011 |
| Ctenopharyngodon idella | EU391390 | Wang et al. 2008 |
| Elopichthys bambusa | AP011213 | Miya et al. 2015 |
| Hypophthalmichthys molitrix | KJ729094 | Farrington et al. 2015 |
| Hypophthalmichthys nobilis | KJ746959 | Farrington et al. 2015 |
| Squaliobarbus curriculus | KC351187 | Liu et al. 2013 |
| Xenocypris argentea | AP011283 | Mayden et al. 2009 |
| Xenocypris davidi | KF039718 | Liu 2014 |
| Ischikauia steenackeri | NC_008667 | Saitoh et al. 2006 |
| Chanodichthys mongolicus | KF826087 | Wei et al. 2016 |
| Chanodichthys ilishaeformis | NC_029722 | Li et al. 2016 |
| Chanodichthys dabryi | NC_021418 | Zhang et al. 2014 |
| Culter erythropterus | NC_024749 | Chen et al. 2016 |
| Culter recurviceps | NC_024277 | GenBank |
| Culter mongolicus | AP009060 | Saitoh et al. 2006 |
| Parabramis pekinensis | KF857485 | Duan et al. 2016 |
| Megalobrama amblycephala | NC_010341 | GenBank |
| Megalobrama pellegrini | NC_026458 | Liu et al. 2016 |
| Hemiculter bleekeri | NC_029831 | GenBank |
| Hemiculter leucisculus | NC_022929 | GenBank |
| Hemiculter eigenmanni | NC_029388 | GenBank |
| Cprinidae | ||
| Cyprinus carpio | AP017363 | Mabuchi 2016 |
| Danionidae | ||
| Rasbora vaterifloris | NC_015531 | Tang et al. 2010 |
| Rasbora lateristriata | NC_032723 | Kusuma & Kumazawa 2016 |
| Rasbora trilineata | NC_025336 | Ho et al. 2016 |
| Rasbora steineri | NC_020005 | Chang et al. 2013 |
| Danio dangila | NC_015525 | Tang et al. 2010 |
| Danio erythromicron | AP011419 | Tang et al. 2010 |
| Danio rerio | NC_002333 | Broughton et al. 2001 |
| Acheilognathidae | ||
| Acheilognathus macropterus | NC_013711 | Hwang et al. 2014 |
| Acheilognathus typus | NC_008668 | Saitoh et al. 2006 |
| Rhodeus ocellatus | NC_011211 | He et al. 2008 |
| Rhodeus lighti | NC_024885 | Wang et al. 2016 |
| Rhodeus sinensis | NC_022721 | Yang et al. 2015 |
| Rhodeus shitaiensis | NC_022690 | Li et al. 2015 |
| Tanakia limbata | NC_025515 | Luo et al. 2016 |
| Tanakia lanceolata | NC_024566 | Xu et al. 2016 |
| Gobionidae | ||
| Hemibarbus barbus | NC_008644 | Saitoh et al. 2006 |
| Squalidus gracilis | NC_024561 | Liu et al. 2016 |
| Abbottina rivularis | NC_023781 | He et al. 2013 |
| Gobio gobio | NC_008662 | Saitoh et al. 2006 |
| Rhinogobio typus | NC_024423 | Yan et al. 2016 |
| Gnathopogon elongatus | NC_008649 | Saitoh et al. 2006 |
| Sarcocheilichthys variegatus microoculus | NC_004694 | Saitoh et al. 2003 |
| Leucisidae | ||
| Leuciscus burdigalensis | NC_029426 | Hinsinger et al. 2015 |
| Acrocheilus alutaceus | AP012086 | GenBank |
| Cyprinella lutrensis | NC_008643 | Saitoh et al. 2006 |
| Macrhybopsis storeriana | NC_030485 | Gaughan et al. 2016 |
| Tincidae | ||
| Tinca tinca | AB218686 | Saitoh et al. 2006 |
| Tanichthys micagemmae | NC_031631 | GenBank |
| Tanichthys albonubes | NC_015539 | GenBank |