#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on November 13, 2026; 6:53 GMT TreeBASE (cc) 1994-2008 Study reference: Li C., Corrigan S., Yang L., Straube N., Harris M., Hofreiter M., White W., & Naylor G. 2015. Capture Reveals Trans Oceanic Gene Flow in Endangered River Sharks. Proceedings of the National Academy of Sciences, U.S.A., . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S18221] [ The following blocks are input data for analysis step 16842 ] BEGIN TAXA; TITLE TaxaForAnalysisStep16842; DIMENSIONS NTAX=20; TAXLABELS Glyphis_fowlerae_GN1363_1 Glyphis_fowlerae_GN1363_2 Glyphis_fowlerae_GN3377_1 Glyphis_fowlerae_GN3377_2 Glyphis_fowlerae_GN4673_1 Glyphis_fowlerae_GN4673_2 Glyphis_gangeticus_GN2668_1 Glyphis_gangeticus_GN2668_2 Glyphis_garricki_GN6502_1 Glyphis_garricki_GN6502_2 Glyphis_garricki_GN6504_1 Glyphis_garricki_GN6504_2 Glyphis_glyphis_GN6505_1 Glyphis_glyphis_GN6505_2 Glyphis_glyphis_GN6506_1 Glyphis_glyphis_GN6506_2 Glyphis_sp_1_GN3681_1 Glyphis_sp_1_GN3681_2 Glyphis_sp_1_GN3682_1 Glyphis_sp_1_GN3682_2 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M33304] TITLE Glyphis_SNPs_Good_Matrix; LINK TAXA = TaxaForAnalysisStep16842; DIMENSIONS NCHAR=1041; FORMAT DATATYPE=Standard SYMBOLS= "0 1 2" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 690 700 710 720 730 740 750 760 770 780 790 800 810 820 830 840 850 860 870 880 890 900 910 920 930 940 950 960 970 980 990 1000 1010 1020 1030 1040 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Glyphis_fowlerae_GN1363_1 00000?000000000000001000?000000010000010000000000000000000001000000000000100?0?000?000000000??000000000000000000100?000000?0100?000000000000000000000000000000?00000000000000000000000000000?0000101000000000000000100?01101000000000000?000000100?0010000000000000000000000000100000000000000000000?0000001000000?10100000000000000000000000?000100001000?0000100000000000000000000000000?0000000000000?000000001010000000000000000100010100000001000000000?000?000000?00100000000000000???0000?0?000?00?000000000000000000000?000000000000100000000?01?0000000?000001010000100000000000000?10000000000?00000000000000010000000000000000000?000100100000000001000000000000000000000000001000000000000000000000?0000?00?0100?000000010000000000100001?0000000000?0??0000100000000010?1000000000000000000000000000000000101000000?00000000000000?000010000000010010000000100000000000000000000010000??0?00000000?00000?000001001000000?000?0?0100?0000000000?100000?100010010000001000?000100000?000000000?00000000000000000000011011000000000?000?0010101?000000?00010000?0000010 Glyphis_fowlerae_GN1363_2 00000?000000100000001000?000000010010010000000000000000000001000000000000100?0?000?000000000??000000000000000000100?000010?0100?000000000000000000000000000000?00000000000000001000000000000?0000101000000000000000100?01101000000000000?010001100?0011000000000100000000000000100000000000000010010?1000001000000?10100000000000000000000000?000100001000?0000101000000000000010000000000?0000000000000?000001001010000000000000000100010100000001000000100?000?000000?00110010000000000???0000?0?000?00?000000100000000000000?000000010000110000000?01?0000000?000001010000100000010000001?10000000000?00000000000000010000000010000000000?000110100000001001000000000010000000000000001000000000000000000001?0010?00?0100?000000010000000000100001?0000000000?0??0001100000000010?1000000000001000010000000000000000101000000?00000000000000?010010000010010010000000100000000000000010000010000??0?00000000?00000?000001001000000?000?0?0100?0000010000?100010?100010011100001000?000111000?000000000?00000000000000000000011011000000000?000?0010111?101000?00010001?0000010 Glyphis_fowlerae_GN3377_1 ?01000000000100000001000?00000001001001000000?000000000000001000000000000100?00000?000000000??000000000000000000100?000000?01000000000000000000000000000000000?000000?0000000001000000000000?000010100000000?000000100?0110100000000000010100011000001000000000000?000000000000100000000000000000000?0000001001000?000000000000000000000000000000100001000100001000000?000000001000000000??0100000000000?000001000010010000000000000100010100000001000000?000000?00?0000001100000000000?000?100000?00000??0000000000000000000000000000000000100000000001?00000000000001010000100000001000001010000000000?00000000000000010000000000000000000100010000000?0000010000000000000000000000000010000000000000000000000000000000000?00000001000000000010000110000000000000?0000100?0000001001000000000000000000000000000000000100000000?00000000000000?000010000000010010000000100000000000000010000010000100?0000000000000010000010?10000000000?0?0100?0000000000?1000000100000010000001000000000100000000000000000000000000000000000110110000000000000101101011000000000010000?0000010 Glyphis_fowlerae_GN3377_2 ?01000000000100000001000?00000001001001000000?000000000000001000000000000100?00001?000000000??000000000000000000100?000000?01000000000000000000000000000000000?000000?0000000001010000000000?010010100000000?000000100?0110100100000000010100011000001000000000000?000000000000100000000000000010000?0001001001000?001000000000000000000000010000100001000100001110000?000100001000000000??1100000000000?000001000010010000000000000100010100000001000000?000000?00?0000001100100000000?000?110000?00000??0000001000000000000000000000000000110000000001?00000001000001010000100000001000001010000000001?00000001000000010000000000000000000100011000000?0010010001000000000001000000000010000000000000000000000001000000100?00000001000000010010000110000000000000?0001100?0000011001000000000001000000000000000000000100000000?00000000000000?000110000010010010000000100000000000000010000010000100?0000000000000010000010?10000000000?0?0100?0001110000?1000000110000011000001000000000100000000000000000000000000000000000110110000000000100101101011000000000011001?0000010 Glyphis_fowlerae_GN4673_1 0000000?00?0100000001000?00000001?010010??0000000000?000000?1000000000000100?0?000??00000000?0000000000000?00000?00000?000?0100?0000?0000?00000?0000000010?0?0?000000?000000000100000??00?00?00001010?00000000?0000?00??11010000?0000?00100000110??0010000??00000??000000000?0010000000?0?0000000000?0000001001000?0?00000000000?0000000?000?00?0100001000?0000100?000?00?000??1000?000000?10000?0000000000?000000010010000000?00000100010?0?0000010000001000?0000000?000010000?00?00000000?000000?0000000000000000?00?00000000?00?0?000000010000?100?01?0000000000000101000010000000?000001?10000000001?0000?0?00000000?00000000100000000001000100?00000001?01001??00?00000000000000000010?00001?0000000?0000?0000000000100?00000001000000??00?000011000000000000?000?1000?0000?00001000000000000000000000?100?00000001000?0000000?000?00??00??00001000?00001??100000?0100000000000000010000010000100?00000000000?00?00000100?000000000??000000?00000000000?00000?1?001??000000010000000?10?000000000000?000000000000?0000?000?10?100000000?00001001?101?000?00??0010000?0000000 Glyphis_fowlerae_GN4673_2 0000000?00?0100000001000?00000001?010110??0100000000?000000?1000000000000100?0?000??00000000?0000000000000?00000?00000?000?0100?0010?0000?00000?0000000010?0?0?000000?000000000100000??00?00?01001010?00000000?0000?00??11010000?0000?00101000110??0010000??00001??000000100?0010000000?0?0000010000?0000001001000?0?10000000010?0000000?000?00?0100001000?0000100?000?01?000??1000?000000?10000?0000000000?001000010010000000?00000100010?0?0000010000001001?0000000?000011001?00?00000000?000000?0000000000001100?00?00000000?00?0?000000011000?100?01?0000000000000101000010000000?000001?10000000001?0000?0?10000000?00000000100000000001010110?00000001?01001??00?00101000000000000010?00001?0000000?0000?0001000000100?00000001000000??00?000011000000000000?000?1000?0000?00001010000000001000000000?101?00000001000?0000000?000?00??00??00001010?01001??100000?0100000000000001010000010000100?00000000000?00?00000100?000000000??000100?00001100000?00100?1?001??100000010000000?10?000000000000?000000000000?0000?000?10?100000000?10001001?101?000?00??0010000?0000001 Glyphis_gangeticus_GN2668_1 0000000000001000000010000000000010010010000000010000000000001000000000000100?00000000000000010000000000000000000100?000000?0100000000000000000000000000000000010000000000000000100000000000010000101000000000000000100101101000000000000101000010000010000?0000000000000000000010000000000000000000010000000001000100000000000000000000000000?0000000010001000010000000000000001000000000011000000000000000000000001000000000000000010001010000000100000000000000000000000110000000000000000000000000000000000000000000000000000000000000000100000000000000000000100001010000000000001000001?1000000000000000000000000001000000000000000000010101000000000000010010000000000000000000000010000001000000000000000000000000100100000001000000000010000110000000000000?000000000000001001000000000000000000000000000000000100000000?00000000000000?0000100000000100000000001000000000000010100000100001000000000000000001000001011000000000000001001000000000001000001100000000000001000000011000000000000000000000000000000000000110110000000000000?0?101011000?00000010000?0000010 Glyphis_gangeticus_GN2668_2 0000000000001000000010000000000010010010000100010000000000001000000000000100?00000000000000010000000000000000000100?000000?0100000000010000000000000000010000010000000000000100100000000000010100101000000000000000100101101000000000000101000110000010000?0000000000000010000010000000000000001000010000001001000100100000000000000000000000?0001000010001000011000000010100001000000010011100010000000000000100001010000000000000010001010000000100000000000000000000001110010000001000000000000000000000000001000000000000000000001000000110000100001000000000100001010000100000001000001?1000000000100000000000000001000000001000000000010101000000000000010010000000100001000010000010000001000000000000000001000000100100000001000000000010000110000000000000?000100000000001001000000000001000000000010000000000100000000?00000000000000?0100100000100100000000001000001000000010100010100001100000000000000001000001011000000000000001101010111000001000001110000000000001000000011000000000000100100000000000000000100110110000000001000?0?101111000?00000010001?0000011 Glyphis_garricki_GN6502_1 ?00000000000000000000000?000000001001000100001000000000000110000000010000100?00000?000110000?00000000000001001000001000000?00000000000001100011110001000010010101110010000000000000100000110?0000000000000000100011000?0100001000000210010011010000010000000000000110000000110000100000000010000000000000000000000?000000000000000000000000001000000000100?0001000110110010000100000000000000000010010001000000000000000100001000000000000?00001000001100001000000010010000000000001000000000000000000010000000000000000000000000101000000000000010010000000000000001000000000001000000000100000010010011000011000000000000010001000100000000001000000000000010010010000000000000000000100000000000000010?001001101010100000?0100000010000010000010000000000000000?1001000000010000000001000000010100000000000000000000000001100001000000001001?00000000010000100001000000000000000100000010000000000000000001010002100101000000000000000101000101000000000?00?00000000001000000001010000?0000100000010010000000000000000000010000000000011000000?00010?00000101100000000?1000100 Glyphis_garricki_GN6502_2 ?00000000000000000000000?000000001001000100101000000000100110000010010000100?01000?000110000?00000000000001001001101000000?00000000000001100011110001000010010101110010001000000000100100110?0100000000000000100011000?0100001000000210010011010000010000000000000110000000110000100000000010000000000000000000000?000000000000000000000000001000000000100?0001000110110111000100000000000000000010010011000000001000000101001000000000000?00001000001100001000000010010000000100001000000000000000000010100000010000000000000000101000000000100010010000000000000001000000010001000001000100000010010011000011000000000000010001100100000000001000000000001010010010010000010000000000100000000000000010?001001101010100000?0100000010000010000010000000000000000?1001010010010000000001000000010100000000000000000000000001100001000000001001?00000000011000100001100000000000000100000010000000000000010001010002100101000000000000000101000101000110000?00?00000100001000000001010000?0000100000010010000000000000000000010000000000011000000?00010?00000101111001001?1000100 Glyphis_garricki_GN6504_1 0000000000000000000000001000000001001000100001000000000000110000000010000100?00000100011000010000000000000100100000?0000000000000000000011000111100010000100?0?0111001000000000000010010011000000000000000000100011000?01000010000001100100010100000100000?00000001100000001000001000000000100000000?0000000000000?000000000000000000000000001000000000100?000100011011001000010100000000?000000010010001000000000000000100001000000000000000001000001100001?0000001001000000000000100000001000000000000000000000000000000000000010100000000000001001000000000000000100000000000100000100010000001001001100001100000000000001000100010000000000100000000000000001001000000000000000000010000000000000001010010?1101010100000?010000001000001000001000000000000000001001010000010000000001000000010100000000000000000000000001100?010000?00010011000000000100001000010000000000000001000000100000000000?0000001010002000101000000000000000?01000101000000000000?00000000?01000000001010000?0000100000010010000000000000000000010000000000011000000?00010?00000101100000000?1000100 Glyphis_garricki_GN6504_2 0000000000000000000000001000001001001100100001000000000000110000000010000100?00001100011000110000000000000100100010?0000100000010000000011000111100010000100?0?0111001000000000000010010011000100000000000000100011000?01000010000002100110110100000100000?00000001100000001000001000000000100010000?0000000000000?000000000001000000000000001000000000100?000101011011001000010100000000?000000010010001100000000000000100001000000000000000001000001100001?0000001001001000010000100000001000000000001000000011000000000000000010100000000010001011000000000000000100000001000100000100010000001001001100001101000000000001000100010000000000101000000000101001001001001001000000000010000000000000001010010?1101010100000?010000001000001000001000000000000100001001010001010010000001000000111100000000000000000000000001100?010000?00010011000000000110001000010000000000000001000000100000000000?0010001010002000101000000000000000?01000101001100000001?00000000?01000000001010000?0000100000010010000000000000000000010000000100011000000?00010?00000101110001001?1000100 Glyphis_glyphis_GN6505_1 001000000000000?0?010?00?000000000000000?0?00100000000000000000100001000000??00101??00001000?0000000000000000101010?0000001000011000010000000101?0010000000000?000000??0000000000000000000000000?000000000?01000001?00?0??000000?00000001001000000000000011000000?10?000000000??000000000000000000000000000000?000?000000000000000010000000001??00??00010000001000?000?0011000100000010000?0000?01000000000??000001000000000100?0000000000000001??0000100000000010000?0000000000000000000?00000000?000000?000000000?00000000000?010000000000?00001000000100000000000?001000000000?00000?00001000000?0001?000000?00000001000000001000000000000101000000000010?0?00000010??0000000000??000000000?0000?000001000000?000000??000?00000?0010000000?0?00000?000000000?00??00?0000000011000?00001000100?000100000000?0000000000000100?0100?00000000000?000000?1010000??00000000?000000001000000?01?0000001000?000001000000000??00100000000000000?000002000000000001000?0?0010000?00001000000?000?0000100000001000100000000?00?0000000000000?000001000010100000?0?000101100?00010?0000000 Glyphis_glyphis_GN6505_2 101000000000000?0?010?00?000000000000000?0?10100000000000000000100001000000??00101??00001000?0000000000000000101010?0000001000011000010000000101?0010000000000?000000??0000000000000000000000010?000000000?01000001?00?0??000000?00000001001000001000000011000000?10?000001000??001000000000000101000000100000?000?000000000000000010000000001??00??10010000001000?000?0011000100000010000?0000?01010000000??000001000000000100?0000000000000001??0000100000000010000?0000000010000000010?00000000?000000?000000100?00000000000?010000000000?10001000000100000000000?001000000000?00000?00001000000?0001?000001?00000001000000001000000101100101000000000011?0?00000010??0000000000??000000000?0000?000001000010?010000??000?00000?0010000000?0?00000?000000000?00??00?0100000011000?00001000100?100100000000?0000000000000100?0100?00000000000?000000?1010000??00000000?000010001000000?01?0000001000?000001000010000??00100000000000010?000002000010100001000?0?0010000?00001000000?000?0000100000101000100000000?00?0000010000000?100001000010100000?0?000101100?01010?0000000 Glyphis_glyphis_GN6506_1 0?1000000000000000010000?0000000000000000000011000000000000?0000000010000000?0?000?000000000?0000000000000000101000100000010000?10000100000001?110000000000100?000?00010000???00000001?0000000000000000000000000000000?000000?0000000000100?000000000000000000000010000000000100000000000000000000000000000000?000?000?00000100000010000?000????0000000100?0001000100000010000?00000010000?0000?01000000000?00000000000?0000000000?000000000000000000010000000001000000?010??00100000000000000000000000000000001000000000001000?000000000000000001000000?000000000000000000000?0000000000000?000000000010010?000000?000100000000100?000000000101000000000000?0000?000?010000000000000000000000000000000?01000000?0100000000?000?00100100000000000000000000000000001000?0?00000011000000?010001000000??00000?0000000000000000?000100000?000000001000000010100000000000?000000000000000?0000110000001000?0000000??00000001001?0000000000010?0?0?0100?00000000?0000000001000000001?000000000?0000100000001000001000000000?0000?00000?00000000?000010?000?0000000?01?000000?0?0000000 Glyphis_glyphis_GN6506_2 0?1000000000000000010000?0000000000000000001011000000000000?0000000110000000?0?101?000001000?0000000000000000101000100000010000?10000100000001?110000100000100?000?00010000???00000001?0000000100000000000000000001000?000000?0000100000100?000000000000110000000010000000000100000000000000000101010000100101?000?000?00000100000010000?000????0000100100?0001010100001111000?00000010001?0000?01010000000?00100010000?0000000010?000000000200001000010010000001000000?010??01100000000000000100000000000000001100000000001000?010010100000010001000100?000000000000001010000?0000000000000?000000000010011?000000?000100000101100?000000100101000000000000?0000?000?010100000000000000000000000001000?01000000?0100000000?000?00100100000000000000000000000100001000?0?00000011000000?010001000100??00000?0000000000000000?000100000?000000001000001010111000000000?000010000001000?0000110001101000?0100010??00000001101?0000000000010?0?0?0100?01010000?0100000001000001001?000000000?0000100000001000011000000000?0100?10000?00000000?000010?000?0000100?01?010000?1?0000000 Glyphis_sp_1_GN3681_1 000001010000010011000101?0001000?000000000101?001001111000000010101000111000?00000?110000001??011000000100011010010?001100?00000010010010000000000000010001000100000000000110100001000000000?0000000110010000010000000?00000000101001000100000001011000000?0000200?010000000?00000000000010001000000?10000000000001010000000010101101010010000000010100010?0100000?0000000000000000000001?00000100000000000000011?0010000000001100100001000010111000101000100000?00?01010000000011100000110?001110110000001001101001000000001110100000000000000000000000?0000010?000000000010000000000001100000010000100?010000?000000000001000001100000000100000001000010001000000011010000010001001000100100000100110001010001?00000000010010001000011100000000010001110000001?10?000001000000000010000000100000001101100000010000000000000010?001000?00000001101000101000000100000000000000001000000000000000000001100000001?0?01001100000000011002101?00100000000000001000?00000000?00001000000000100?0000010100000001000100000101000001000000001000000000000?10000000010?00?0000110010000100 Glyphis_sp_1_GN3681_2 000101010000010011000101?0001000?000000000101?001011111010000010101000111000?00000?111000001??011000000101011010010?001101?00000010010010000000000000010001000100000000000110100001000000000?0100000110010000010000000?00000000101001000100000001011000000?1000200?010010010?00000000000010001010000?10000000000001010000000010101101010010000000010100010?0100010?0100000000000000000001?00010100000000000001111?0010000000101100100011000010111000101000100000?01?01010000000011100000110?001110110000001001101001000001101110100000000000010000000000?0000110?000000000010000000000001100000010000100?010000?000000000001000001100010000100000001001010001000000011010000011001001000100100000100110011110001?01000010010010001000011100000000011001110000001?10?010001000000000010000000100000001101100000010000000000000010?001000?00000001101000101010000101000000000000001010000000000000000001100000001?0?01001100000000011002101?00100000001110001000?00000000?00001000000100100?0000010100000001000100000101000001100000001000000000000?10000000010?00?0100110110000100 Glyphis_sp_1_GN3682_1 000001010000010011000101?000100000000000001011001000110000000010101000111000100000?110000000??011000000101011010000?001100?00000010010010000000000000010001000?00000000000010100001000000000?0000000110010000010000000?00000000101000000100000001010000000000002000010000000000000000000010001000000?1000000000000101000000001010110101001000?0?00100000100010000010000000000000000000001??0010100000000000?000010000000000000110010001100001011100010000?1000000000000100000000111000001100001110?10000001001101001000001001110100000000000010000000000000000100000000000010000000000001100000010000100?01000010000000000010000001000000001000000010000?000?00000001101000001000100100010010000010011000?010001?00000010010?1000100001110000000001000111000000111??0100000?0000000010000000100000001101100000010000000000000010000100010000000?10100010100000010000000000000000100000000000000000000110000000100?01000100000000011002101?0?1000?0000000001?00000000000000001000000000100?000001010000000100000000010100000100000000100000?000000?10000000010?00100000100?0000100 Glyphis_sp_1_GN3682_2 100001010000010011000101?000100000000000001011001000111000000010101000111000100001?111000000??011000000101011010010?001101?00000010010010000000000000010001000?00000000000110100001000000000?0100010110010000010000000?00000000101001001110000001011000000000002000010000000000000000000010001010100?1000001000000101000100001010110101001000?0?00100000100010000010100000001000000000001??0010100000000000?001110001000000000110010001100001011100010100?1000000010010101000000111000001100001110?10000001001101001000001101110100000000000010000000000001001100000000000010000000000001100000010000100?01000010000000000010000001000000001000000011010?001?00000001101010101000100100010010000010011000?010001?01000010010?1000100001110000000001000111000000111??0100110?0000010010000000100000001101100000010000000000000010000100010000000?10100010101000010100000000000000101001000000000000000110000000100?01000100000000011002101?0?1000?0001010001?00100000000000001000000000100?000001010000000100010000010100000110100000100000?000000?10000000010?00101001100?0000100 ; END; [ The following blocks are output data for analysis step 16842 ] BEGIN TREES; TITLE Glyphis_SNPs_Good_Result; LINK TAXA = TaxaForAnalysisStep16842; TREE SNAPP_tree = [&R] ((((Glyphis_glyphis_GN6505_1:5.21E-4,Glyphis_glyphis_GN6506_1:5.21E-4):0.011327,(Glyphis_garricki_GN6504_1:1.68E-4,Glyphis_garricki_GN6502_1:1.68E-4):0.01168):84.493121,(((Glyphis_gangeticus_GN2668_1:5.73E-4,Glyphis_fowlerae_GN4673_1:5.73E-4):5.19E-4,Glyphis_fowlerae_GN3377_1:0.001091):4.5E-4,Glyphis_fowlerae_GN1363_1:0.001541):84.503428):21.191135,(Glyphis_sp_1_GN3681_1:3.78E-4,Glyphis_sp_1_GN3682_1:3.78E-4):105.695726); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr90390] END;