Additional file 1: Table S1. List of studied specimens ...

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Melanotaenia lacustris. Melanotaenia lacustris. Melanotaenia macchullochi. Melanotaenia papuae. Melanotaenia praecox. Melanotaenia sexlineata "Kiunga".
Iso rhotophilus Atherinomorus endrachtensis Atherinomorus lacunosus Craterocephalus honoriae Hypoatherina tsurugae Quirichthys sp. Quirichthys sp. Atherinella panamensis Bedotia sp. Bedotia sp. Chilatherina bleheri Chilatherina campsi Chilatherina fasciata Chilatherina fasciata Chilatherina fasciata Chilatherina sp. Glossolepis dorityi Glossolepis maculosus Glossolepis pseudoincisus Glossolepis romuensis Melanotaenia affinis "Lae" Melanotaenia affinis "Pagwi" Melanotaenia angfa Melanotaenia angfa Melanotaenia australis Melanotaenia batanta Melanotaenia boesemani Melanotaenia cf. eachamensis Melanotaenia douboulayi Melanotaenia goldiei "Tapini" Melanotaenia herbertaxelrodi Melanotaenia lacustris Melanotaenia lacustris Melanotaenia macchullochi Melanotaenia papuae Melanotaenia praecox Melanotaenia sexlineata "Kiunga" Melanotaenia sexlineata "Tabubil" Melanotaenia splendida inornata Melanotaenia splendida inornata

Notocheiridae Atherinidae

Melanotaeniidae

Atherinopsidae Bedotiidae

Species

Family

Voucher no. or GenBank no.1 ZSM (RS10)* ZSM (RS3)* ZSM (RS5)* ZSM (RS6)* AP004420 ZSM 34172-1 ZSM 34172-3 ZSM (RS4)* ZSM 34169 ZSM 34168 ZSM 34140 ZSM 34177 ZSM 34137 ZSM 34142 ZSM 34141 ZSM 34143 ZSM (IS50)* ZSM 34147 ZSM (IS52)* ZSM (IS51)* ZSM 34138 ZSM 34146 ZSM 34148 ZSM 34149 ZSM (IS57)* ZSM 34535 ZSM 34153 ZSM 34158 ZSM (IS54)* ZSM 34174 ZSM (IS53)* AP004419 ZSM (IS58)* ZSM (IS61)* ZSM 34151 ZSM (IS55)* ZSM 34155 ZSM 34154 ZSM 34167 ZSM 34161 Australia Indo-Pacific Japan Australia Gregory River, Queensland, Australia Gregory River, Queensland, Australia Gregory River, Queensland, Australia Panama (Eastern Pacific) Ankavia, Madagascar (AS) Lazana, Madagascar (AS) Papua New Guinea (AS) Papua New Guinea (AS) Clearwater Creek, Papua New Guinea (AS) Lake Wanam, Papua New Guinea (AS) Lake Sentani, West Papua, Indonesia (AS) Mamberamo River, West Papua, Indonesia (AS) Lake Nenggwambu, West Papua, Indonesia (AS) Aquarium stock Tami River System, Lake Yaniruk, West Papua, Indonesia (AS) Ramu River System, Papua New Guinea (AS) Aquarium stock Aquarium stock Aquarium stock Aquarium stock Northern Australia (AS) Batanta Island, West Papua, Indonesia (AS) Lake Aitinyo, West Papua, Indonesia (AS) upper Barron River, Queensland, Australia (AS) Eastern Australia (AS) Aquarium stock Lake Tebera, Papua New Guinea (AS) Lake Kutubu, Papua New Guinea (AS) Lake Kutubu, Papua New Guinea (AS) Eastern Australia (AS) Aquarium stock Mamberamo River System, West Papua, Indonesia (AS) Aquarium stock Aquarium stock Adelaide River, Northern Territory, Australia (AS) Blyth River, Northern Territory, Australia (AS)

Locality/distribution (AS = Aquarium stock)

Additional file 1: Table S1. List of studied specimens including distribution information and accession numbers Accession no. ND2 KJ667882 KJ667867 KJ667868 KJ667877 [59] KJ667922 KJ667923 KJ667866 KJ667870 KJ667869 KJ667872 KJ667873 KJ667874 KJ667876 KJ667875 KJ667871 KJ667878 KJ667879 KJ667880 KJ667881 KJ667888 KJ667889 KJ667890 KJ667891 KJ667892 KJ667893 – KJ667894 KJ667895 KJ667896 KJ667897 – KJ667898 KJ667899 KJ667900 KJ667901 KJ667903 KJ667902 KJ667908 KJ667904

Accession no. 12S-16S KJ667787 KJ667772 KJ667773 KJ667782 [59] KJ667824 KJ667825 KJ667771 KJ667775 KJ667774 KJ667777 KJ667778 KJ667779 KJ667781 KJ667780 KJ667776 KJ667783 KJ667784 KJ667785 KJ667786 KJ667789 KJ667790 KJ667791 KJ667792 KJ667793 KJ667794 KJ667795 KJ667796 KJ667797 KJ667798 KJ667799 [59] KJ667800 KJ667801 KJ667802 KJ667803 KJ667805 KJ667804 KJ667810 KJ667806

Telmatherinidae

Pseudomugilidae

Melanotaenia splendida inornata Melanotaenia splendida inornata Melanotaenia splendida inornata Melanotaenia splendida splendida Melanotaenia trifasciata "Hapgood River" Melanotaenia trifasciata Melanotaenia trifasciata Rhadinocentrus ornatus Pseudomugil furcatus Pseudomugil pellucidus Pseudomugil reticulatus Pseudomugil signifer Kalyptatherina helodes Kalyptatherina helodes Kalyptatherina helodes Kalyptatherina helodes Marosatherina ladigesi Paratherina cf. labiosa Paratherina cf. labiosa Paratherina cf. striata Paratherina cf. striata Paratherina striata Telmatherina sarasinorum Telmatherina sarasinorum Telmatherina sarasinorum Telmatherina sarasinorum Telmatherina abendanoni Telmatherina abendanoni Telmatherina antoniae Telmatherina antoniae Telmatherina antoniae Telmatherina antoniae Telmatherina antoniae Telmatherina bonti Telmatherina bonti Telmatherina bonti Telmatherina bonti Telmatherina bonti Telmatherina bonti Telmatherina bonti Telmatherina bonti Telmatherina celebensis Telmatherina celebensis Telmatherina celebensis Telmatherina celebensis

ZSM 34165 ZSM 34163 ZSM 34166 ZSM 34160 ZSM 34180 ZSM 34182 ZSM 34157 ZSM 34156 ZSM (IS68)* ZSM (IS63)* ZSM 34170 ZSM (IS66)* MZB 17152-1 MZB 17152-2 MZB 22095-1 MZB 22095-2 ZSM 34735 ZSM 33054 ZSM 33055 ZSM 33057 ZSM 33061 ZSM 33062 ZSM 33115 ZSM 33116 ZSM 33117 ZSM 33127 ZSM 33118 ZSM (T26)* ZSM 33089 ZSM 33090 ZSM 33092 ZSM 33093 ZSM 33100 ZSM 33067 ZSM 33068 ZSM 33070 ZSM 33128 ZSM 33129 ZSM 33160 ZSM (T85)* ZSM (T86)* ZSM 33071 ZSM 33072 ZSM 33078 ZSM 33079

Flat Rock Creek, New South Wales, Australia (AS) Goyder Creek, Northern Territory, Australia (AS) Mann River, New South Wales, Australia (AS) Deepwater Creek, Queenslands, Australia (AS) Aquarium stock Pappan Creek, Queensland, Australia (AS) Wonga Creek, Norther Territory, Australia (AS) Coolum Creek, Queensland, Australia (AS) Aquarium stock Aquarium stock Aquarium stock Aquarium stock Batanta, west of New Guinea Batanta, west of New Guinea Misool, west of New Guinea Misool, west of New Guinea Maros karst, SW Sulawesi, Indonesia Lake Mahalona, Sulawesi, Indonesia Lake Mahalona, Sulawesi, Indonesia Lake Mahalona, Sulawesi, Indonesia Lake Towuti, Sulawesi, Indonesia Lake Mahalona, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Stream close by Malili, Central Sulawesi, Indonesia Stream close by Malili, Central Sulawesi, Indonesia Tominanga River (connecting Mahalona-Towuti), Sulawesi, Indonesia Nuha, Lake Matano, Sulawesi, Indonesia Nuha, Lake Matano, Sulawesi, Indonesia Tominanga River (connecting Mahalona-Towuti), Sulawesi, Indonesia Lake Towuti, Sulawesi, Indonesia Lake Towuti, Sulawesi, Indonesia Lake Mahalona, Sulawesi, Indonesia Lake Towuti, Sulawesi, Indonesia Lake Mahalona, Sulawesi, Indonesia Lake Towuti, Sulawesi, Indonesia

KJ667906 KJ667905 KJ667907 KJ667909 KJ667911 KJ667912 KJ667910 KJ667924 KJ667918 KJ667919 KJ667920 KJ667921 KJ667883 KJ667884 KJ667885 KJ667886 KJ667887 KJ667913 KJ667914 KJ667915 KJ667916 KJ667917 KJ667957 KJ667954 KJ667955 KJ667956 KJ667926 KJ667925 KJ667927 KJ667928 KJ667929 KJ667930 KJ667931 KJ667934 KJ667935 KJ667936 KJ667937 KJ667938 KJ667939 KJ667932 KJ667933 KJ667940 KJ667941 KJ667942 KJ667943

KJ667808 KJ667807 KJ667809 KJ667811 KJ667813 KJ667814 KJ667812 KJ667826 KJ667820 KJ667821 KJ667822 KJ667823 – – – – KJ667788 KJ667815 KJ667816 KJ667817 KJ667818 KJ667819 KJ667859 KJ667856 KJ667857 KJ667858 KJ667828 KJ667827 KJ667829 KJ667830 KJ667831 KJ667832 KJ667833 KJ667836 KJ667837 KJ667838 KJ667839 KJ667840 KJ667841 KJ667834 KJ667835 KJ667842 KJ667843 KJ667844 KJ667845

ZSM 33126 ZSM (T53)* ZSM (T54)* ZSM 33120 ZSM 33153 ZSM 33154 ZSM 33157 ZSM 33097 ZSM 33106 ZSM 33110 ZSM 33121 ZSM 33122 ZSM 33151 ZSM (T33)* ZSM 33133 ZSM 33134

Lake Matano, Sulawesi, Indonesia Petea River (connecting Matano-Mahalona), Sulawesi, Indonesia Petea River (connecting Matano-Mahalona), Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Matano, Sulawesi, Indonesia Lake Mahalona, Sulawesi, Indonesia Lake Mahalona, Sulawesi, Indonesia

KJ667944 KJ667945 KJ667946 KJ667947 KJ667948 KJ667949 KJ667950 KJ667951 KJ667952 KJ667953 KJ667958 KJ667959 KJ667961 KJ667960 KJ667962 KJ667963

KJ667846 KJ667847 KJ667848 KJ667849 KJ667850 KJ667851 KJ667852 KJ667853 KJ667854 KJ667855 KJ667860 KJ667861 KJ667863 KJ667862 KJ667864 KJ667865

MZB = Museum Zoologicum Bogoriense, Bogor; ZSM = Zoologische Staatssammlung München (Bavarian State Collection of Zoology, Munich); * = no voucher material available.

1

Telmatherina cf. obscura Telmatherina cf. wahjui Telmatherina cf. wahjui Telmatherina opudi Telmatherina opudi Telmatherina opudi Telmatherina opudi Telmatherina prognatha Telmatherina prognatha Telmatherina prognatha Telmatherina sp. Telmatherina sp. Telmatherina wahjui Telmatherina wahjui Tominanga sp. Tominanga sp.