#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 May 19, 2024; 6:35 GMT TreeBASE (cc) 1994-2008 Study reference: Rothfels C., Johnson A.K., Windham M.D., & Pryer K. 2014. Low-copy nuclear data confirm rampant allopolyploidy in the Cystopteridaceae (Polypodiales). Taxon, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S15964] BEGIN TAXA; TITLE 'Cystopteridaceae_gapCpSh_alleles'; DIMENSIONS NTAX=48; TAXLABELS 'Acystopteris taiwaniana 4870 c2 3 4 6 [5]' 'Acystopteris tenuisecta 4831 Tai c1 4 6 [3]' Cystopteris_bulbifera_5836_Arz_c1_5_7_627 'Cystopteris bulbifera 6116 On c12 [2_4_5_9_14_10_11_15_1_3_8_7]' 'Cystopteris fragilis 5316 CR c1 2 9 [12_14 5 6 8 11_4_7_10]' 'Cystopteris fragilis 5840 Swd c2 4 [1_9]' 'Cystopteris fragilis 5840 Swd c6 8 10 [3_5_7]' 'Cystopteris fragilis 5851 Ut c1 2 12 13 [3_4_5_9]' Cystopteris_fragilis_5851_Ut_c10_576 'Cystopteris fragilis 5851 Ut c7 11 14 16 [6_8]' Cystopteris_fragilis_5951_Col_c11_593 'Cystopteris fragilis 5951 col c4 5 8 12 13 17 18 20 22 23 [9_10_12_14_15_19_3_21]' 'Cystopteris fragilis 5951 col c6 [1]' 'Cystopteris fragilis 6380 Arg c1 [2_5_6]' Cystopteris_fragilis_6380_Arg_c4_588_short 'Cystopteris fragilis 7009 Iceland c10 15 [9_19]' 'Cystopteris fragilis 7009 Iceland c7 12 13 14 16 [3_6_8_17_2_11_4_5]' 'Cystopteris fragilis 7248 Switz c2 [3_7]' 'Cystopteris fragilis 7248 Switz c4 5 6 [1]' 'Cystopteris fragilis 7625 Taiwan c1 [6]' 'Cystopteris fragilis 7625 Taiwan c2 4 [3_5]' 'Cystopteris montana 5839 NFD c1 [5_4_7]' 'Cystopteris moupinensis 4861 Tai c4 [1_2_3_5]' 'Cystopteris protrusa 5838 Mis c1 [4]' 'Cystopteris protrusa 5838 Mis c2 5 [3]' Cystopteris_tasmanica_6379_NZ_c1_603 'Cystopteris tenuis 6387 VT c1 4 8 14 [3_6]' 'Cystopteris tenuis 6387 VT c10 [7_11_12]' 'Gymnocarpium appalachianum 7639 Virg c2 4 6 10 [1_5_7_9]' 'Gymnocarpium appalachianum 7800 Virg c9 12 [1_11_10_14_8_15_2_16_17]' 'Gymnocarpium disjunctum 4710 ALSK c2 [1_3_4]' 'Gymnocarpium disjunctum 7751 Wash c2 5 9 13 [11_12]' 'Gymnocarpium disjunctum 7751 Wash c6 [1_10_14_15]' Gymnocarpium_dryopteris 'Gymnocarpium dryopteris 5837 Fin c1 2 [3]' Gymnocarpium_dryopteris_5837_Fin_c4_5_6_7_658bp Gymnocarpium_dryopteris_7981_Japan_c16_19_658 'Gymnocarpium dryopteris 7981 Japan c2 5 10 12 [1_4_7_11_13_18]' 'Gymnocarpium dryopteris 7981 Japan c3 6 [8_9_15_17]' 'Gymnocarpium dryopteris 8031 Ont c6 [4_5]' Gymnocarpium_jessoense_parvulum_6979_Ont_c1_658 Gymnocarpium_jessoense_parvulum_6979_Ont_c3_c4_658 'Gymnocarpium jessoense parvulum 8120 Russia c1 2 3 7 10 12 [5_11]' 'Gymnocarpium jessoense parvulum 8120 Russia c6 8 9 [4]' Gymnocarpium_remotepinnatum_4862_Tai_c3_658 'Gymnocarpium remotepinnatum 4862 Tai c4 6 7 [1_2_5]' 'Gymnocarpium robertianum 7945 Norw c4 12 13 14 [3_7_10_9_11]' 'Gymnocarpium robertianum 7945 Norw c5 8 [1]' ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M22807] TITLE gapCpSh_alleles_Codonposition3; LINK TAXA = 'Cystopteridaceae_gapCpSh_alleles'; DIMENSIONS NCHAR=99; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 ] [ . . . . . . . . . ] 'Acystopteris taiwaniana 4870 c2 3 4 6 [5]' CGAAAGCTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAATACCGATGGTATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCTTGTAGTTG 'Acystopteris tenuisecta 4831 Tai c1 4 6 [3]' CGAAAGCTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAATACCGATGGTATATCGAATGACTATTTACTCTTTTAAACATTTAACTCCTTGTAGTTG Cystopteris_bulbifera_5836_Arz_c1_5_7_627 TGAAAGGTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCCTGTAGTTG 'Cystopteris bulbifera 6116 On c12 [2_4_5_9_14_10_11_15_1_3_8_7]' TGAAAGGTAGATGGCTAGACAGTCCTCGTGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCCTGTAGTTG 'Cystopteris fragilis 5316 CR c1 2 9 [12_14 5 6 8 11_4_7_10]' CGAAAGGTAGATAGCTAGACAGTCCTCATGCGTCCAGAGAACTTCGATGGTATATCGAATTACTATTTACTCTCTTAAACACTTAACTCCTTGTAGTTG 'Cystopteris fragilis 5840 Swd c2 4 [1_9]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris fragilis 5840 Swd c6 8 10 [3_5_7]' CGAAAGGTAGATGGCTAGACAGTCCTCGTGCGTCCAGAAAACTCCGATGGCATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCCTGTAGTTG 'Cystopteris fragilis 5851 Ut c1 2 12 13 [3_4_5_9]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTG Cystopteris_fragilis_5851_Ut_c10_576 CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTCTCAAACATTTGACTCCCTGTAGTTG 'Cystopteris fragilis 5851 Ut c7 11 14 16 [6_8]' CGAAAGGTAGATAGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCTTGTAGTTG Cystopteris_fragilis_5951_Col_c11_593 CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris fragilis 5951 col c4 5 8 12 13 17 18 20 22 23 [9_10_12_14_15_19_3_21]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris fragilis 5951 col c6 [1]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTCTCAAACATTTGACTCCCTGTAGTTG 'Cystopteris fragilis 6380 Arg c1 [2_5_6]' CGAAAGGTAGATAGCCAGACAGTCCTCATGCGTCCAGAGAACTTCGATGGTATATCGAATTACTATTTACTCTCTTAAACACTTAACTCCTTGTAGTTG Cystopteris_fragilis_6380_Arg_c4_588_short CGAAAGGTAGATAGCTAGACAGTCCTCATGCGTCCAGAGAACTTCGATGGTATATCGAATTACTATTTACTCTCTTA---------------------- 'Cystopteris fragilis 7009 Iceland c10 15 [9_19]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris fragilis 7009 Iceland c7 12 13 14 16 [3_6_8_17_2_11_4_5]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTGCGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris fragilis 7248 Switz c2 [3_7]' CGAAAGGTAGATGGCTAGACAGTCCTCGTGCGTCCAGAAAACTCCGATGGCATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCCTGTAGTTG 'Cystopteris fragilis 7248 Switz c4 5 6 [1]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTC 'Cystopteris fragilis 7625 Taiwan c1 [6]' CGAAAGGTAGATAGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris fragilis 7625 Taiwan c2 4 [3_5]' CGAAAGGTAGATGGCTAGACAGTCCTCATGCGTCCAGAAAACTCCGATGGTATATCGAATGACTATTTACTCTCTTAAACACTTAACTCCCTGTAGTTG 'Cystopteris montana 5839 NFD c1 [5_4_7]' CGAAAGGTAGATGGCTAGACAGTCCTCATGCGTTCAGAGAATTCCGATGGTATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCCTGTAGTTG 'Cystopteris moupinensis 4861 Tai c4 [1_2_3_5]' CGAAAGGTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTTTTAAACATTTAACTCCCTGTGGTTG 'Cystopteris protrusa 5838 Mis c1 [4]' CGAAAGGTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTTCGATGGTATATCGAATGACTATTTACCCTTTTAAACATTTAACTCCCTGTAGTTG 'Cystopteris protrusa 5838 Mis c2 5 [3]' CGAAAGGTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTTCGATGGTATATCGAATGACTATTTACCCTTTTAAACATTTAACTCCCTGTAGTTG Cystopteris_tasmanica_6379_NZ_c1_603 CGAAAGGTAGATAGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATAACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris tenuis 6387 VT c1 4 8 14 [3_6]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTGCGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris tenuis 6387 VT c10 [7_11_12]' CGAAAGGTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTTCGATGGTATATCGAATGACTATTTACCCTTTTAAACATTTAACTCCTTGTAGTTG 'Gymnocarpium appalachianum 7639 Virg c2 4 6 10 [1_5_7_9]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium appalachianum 7800 Virg c9 12 [1_11_10_14_8_15_2_16_17]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTTTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium disjunctum 4710 ALSK c2 [1_3_4]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAGTATTAAACTCCTTGTAGTTG 'Gymnocarpium disjunctum 7751 Wash c2 5 9 13 [11_12]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAATATTAAACTCCTTGTAGTTG 'Gymnocarpium disjunctum 7751 Wash c6 [1_10_14_15]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAGTATTAAACTCCTTGTAGTTG Gymnocarpium_dryopteris CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium dryopteris 5837 Fin c1 2 [3]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG Gymnocarpium_dryopteris_5837_Fin_c4_5_6_7_658bp CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAGTATTAAACTCCTTGTAGTTG Gymnocarpium_dryopteris_7981_Japan_c16_19_658 CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium dryopteris 7981 Japan c2 5 10 12 [1_4_7_11_13_18]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAATATTAAACTCCTTGTAGTTG 'Gymnocarpium dryopteris 7981 Japan c3 6 [8_9_15_17]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAGTATTAAACTCCTTGTAGTTG 'Gymnocarpium dryopteris 8031 Ont c6 [4_5]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAGTATTAAACTCCTTGTAGTTG Gymnocarpium_jessoense_parvulum_6979_Ont_c1_658 CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG Gymnocarpium_jessoense_parvulum_6979_Ont_c3_c4_658 CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCTACTCTTTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium jessoense parvulum 8120 Russia c1 2 3 7 10 12 [5_11]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCTACTCTTTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium jessoense parvulum 8120 Russia c6 8 9 [4]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG Gymnocarpium_remotepinnatum_4862_Tai_c3_658 CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTTTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium remotepinnatum 4862 Tai c4 6 7 [1_2_5]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium robertianum 7945 Norw c4 12 13 14 [3_7_10_9_11]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTTTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium robertianum 7945 Norw c5 8 [1]' CGAAAGGTAGGCGGCTAGACAGTCCCCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTACCCACTCTCTTAAACATTAAACTCCCTGTAGTTG ; END;