#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 April 19, 2024; 1:00 GMT TreeBASE (cc) 1994-2008 Study reference: Santos S., Taylor D., & Coffroth M. 2001. Genetic comparisons of freshly isolated vs. cultured symbiotic dinoflagellates: Implications for extrapolation to the intact symbiosis. Journal of Phycology, 37(5): 900-912. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S740] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=24; TAXLABELS Briareum_asbestinum_in_hospite_FL Eunicea_sp_in_hospite_12_Ft_Mound_FL Gorgonia_sp_in_hospite_12_Ft_Mound_FL Plexaura_flexuosa_culture_Tennessee_Reef_FL Plexaura_flexuosa_in_hospite_Tennessee_Reef_FL Plexaura_homomalla_in_hospite_San_Blas_Panama Plexaura_kuna_culture_#13_FL Plexaura_kuna_culture_#702_San_Blas_Panama Plexaura_kuna_culture_#704_San_Blas_Panama Plexaura_kuna_culture_#706_San_Blas_Panama Plexaura_kuna_in_hospite_12_Ft_Mound_FL Plexaura_kuna_in_hospite_Bache_FL Plexaura_kuna_in_hospite_Bahamas Plexaura_kuna_in_hospite_Niantupo_Panama Plexaura_kuna_in_hospite_North_Bocas_Panama_colony_1 Plexaura_kuna_in_hospite_North_Bocas_Panama_colony_3 Plexaura_kuna_in_hospite_San_Blas_Panama Plexaura_kuna_in_hospite_South_Bocas_Panama_colony_2 Plexaura_kuna_in_hospite_South_Bocas_Panama_colony_7 Plexaura_kuna_in_hospite_St_Croix_US_Virgin_Islands Pseudoterogorgia_americana_in_hospite_FL Pseudoterogorgia_elisabethae_culture_Bahamas Pseudoterogorgia_elisabethae_in_hospite_Bahamas Symbiodinium_kawagutii ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2315] TITLE Symbiodinium_Clade_B_rDNA_ITS; LINK TAXA = Taxa1; DIMENSIONS NCHAR=691; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=N 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Briareum_asbestinum_in_hospite_FL GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTTGACACTGTG-ACTTTTGACGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGCGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCGGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAATTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGT----CTACACTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCGTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTAGCTTGCATCGTA----CAGCTCAAGCGCGCAGCTGTTGGG-ATGCTGATGCATGCCCTTAGCATGAA Eunicea_sp_in_hospite_12_Ft_Mound_FL GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAG-TGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCACGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Gorgonia_sp_in_hospite_12_Ft_Mound_FL GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGC-CGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAG-TTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_flexuosa_culture_Tennessee_Reef_FL GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGCGACAGCGGTGCATCGGCGCCTGGT---GCATCTGGCACCGGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCA-CGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGT----CTACACTGCTGCTTTGCTTTCCAACAAGTCATCGATCGCGTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTAGCTTGCATCGTA----CAGCTCAAGCGCGCAGCTGTTGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_flexuosa_in_hospite_Tennessee_Reef_FL GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATC----ACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCA-CGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCACGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_homomalla_in_hospite_San_Blas_Panama GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCCTCTGGCACCAGGCGGGCCTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTTGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGG-CGCAGCGAAGCGCGA-TAGTCTTTCTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCACGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_kuna_culture_#13_FL GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAG-TGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_kuna_culture_#702_San_Blas_Panama GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACATTGTG-ACTTTTGACGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCGGGCGCGGGTGTTGCCCTGTGGCC--GGGTTGAGCTCTAGGG-----TGAGATAGTCA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTCTGCTTGCAAGCAGCATGTA----TACACTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCGTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTAGCTTGCATCGTACGTACAGCTCAAGCGCGCAGCTGTTGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_kuna_culture_#704_San_Blas_Panama GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGAGGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGTATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_kuna_culture_#706_San_Blas_Panama GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGCGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-GGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_kuna_in_hospite_12_Ft_Mound_FL GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAG-TGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_kuna_in_hospite_Bache_FL GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAG-TGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCACGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_kuna_in_hospite_Bahamas GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCACGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_kuna_in_hospite_Niantupo_Panama GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAG Plexaura_kuna_in_hospite_North_Bocas_Panama_colony_1 GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAG-TGAACCTCGGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGGGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCACGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_kuna_in_hospite_North_Bocas_Panama_colony_3 GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAG-TGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCGCCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCACGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_kuna_in_hospite_San_Blas_Panama NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCCTCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCACGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTNNNNNNNNNNNNNNNNNNNNN Plexaura_kuna_in_hospite_South_Bocas_Panama_colony_2 GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAG-TGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_kuna_in_hospite_South_Bocas_Panama_colony_7 GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAG-TGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGGC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGAAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCACGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Plexaura_kuna_in_hospite_St_Croix_US_Virgin_Islands GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAG-TGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCAGCGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Pseudoterogorgia_americana_in_hospite_FL GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCA-CGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Pseudoterogorgia_elisabethae_culture_Bahamas GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAG-TGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCA-CGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Pseudoterogorgia_elisabethae_in_hospite_Bahamas GTGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAG-TGAACCTGCGGAAGGATCATTCGCACTGAT-CAACTCTCGACACTGTG-ACTTTTGATGTGAGGGACGCTTGTGGTGAAATATCTGCTTGCGGAACTCGTGGGTGACAGCGGCGCATCGGCGCCTGGT---GCATCTGGCACCAGGCGCGGGTGTTGCCCTGTGGCC--GGGTT-AGCTCTAGGG-----TGAGATAGTTA----------GCGCAAGCTTTCTGGAAAGGATGATGGTCCAAAA-CTACAACTTTCAGTGATGGATATCTTGGCTCGGGCACCTTTGAAGGGCGCA-CGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCGATGGCCTCCTGAACGCGCATTGCGCTCTCGGGATTTCCTGAGAGCAGGTCTGCTTCAGTGCTTAGCATTATCTACCTGTGCTTGCAAGCAGCATGTATGTCTGCATTGCTGCTTCGCTTTCCAACAAGTCATCGATCGCTTTTGTGTTCGTAAATGGCTTGTTTGCTGCCTGGCCCATGCGCCAAGCTTGAGCGTACTGTTGTTCCAA---GCTTTGCTTGCATCGTG----CAGCTCAAGCGCGCAGCTGTCGGG-ATGCTGATGCATGCCCTTAGCATGAA Symbiodinium_kawagutii GCGTTGGAAAGTTTCATGAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTCGCACTGATTCAACTCTGACCAT-GTGAACTTTGGTTGTGAGGGATGCTTGCGGTGAGATATCTGCTTGCTGAACTCGTGGGCGACAGAGGCACATCGGCAGCCAGCAGCGCATCTGC--CCTGGCGCTGGTGTCGCCCTGTGGTCAAGGGTC-CACTGTGTGGGCCGTTGCTATAGTAATGAGATTTTTGTGCAAGCTGTCTGACAAGGACATTGGTCCAAATTCCACAACTTTCAGTGATGGATGTCTTGGCTCAAGCACCTGTGAAGGGCGCA-CGAAGCGCGA-TAGTCTTTGTGAATTGCAGAACTCCGTGAACCAATGGCCGCCTGAACGTACGTTGCACTCTTGGGATTTCCTGAGAGTATGTCTGCTTCAGTGCTTAGC-----TTGCCCAATCTTGCGGATAGATTTTGTTTCTGTCTTGCGCCCCTGTGAGCCATTGAAACTCTAGTCAA---TGGCTTATTGAATGAGTTGGTC-TTGCAAAAGCTTTGCGCGATGCTATTCAAGATTCCCCCTTGAAATGGCATTTCTTGAGTGACG----CTGCTTATGCTTGCAACTGCTGGG-ATGCTAGCGCATGCCTCTAGCATGAA ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = Symbiodinium_Clade_B_rDNA_ITS) = N: 1-691; CODONPOSSET CodonPositions (CHARACTERS = Symbiodinium_Clade_B_rDNA_ITS) = N: 1-691; END; BEGIN ASSUMPTIONS; WTSET * weigh gaps by length = 0.25: 203-206 , 0.2: 505-509 ; WTSET weigh gaps by length = 0.2: 505-509 , 0.25: 203-206 ; END; BEGIN TREES; TITLE Tb5923; LINK TAXA = Taxa1; TRANSLATE 1 Plexaura_kuna_in_hospite_Niantupo_Panama, 2 Plexaura_kuna_in_hospite_North_Bocas_Panama_colony_1, 3 Plexaura_kuna_in_hospite_North_Bocas_Panama_colony_3, 4 Plexaura_kuna_in_hospite_South_Bocas_Panama_colony_2, 5 Plexaura_kuna_in_hospite_South_Bocas_Panama_colony_7, 6 Plexaura_kuna_in_hospite_Bache_FL, 7 Plexaura_kuna_in_hospite_12_Ft_Mound_FL, 8 Plexaura_kuna_in_hospite_St_Croix_US_Virgin_Islands, 9 Plexaura_kuna_culture_#13_FL, 10 Briareum_asbestinum_in_hospite_FL, 11 Plexaura_kuna_in_hospite_San_Blas_Panama, 12 Plexaura_kuna_culture_#706_San_Blas_Panama, 13 Pseudoterogorgia_elisabethae_in_hospite_Bahamas, 14 Plexaura_flexuosa_in_hospite_Tennessee_Reef_FL, 15 Gorgonia_sp_in_hospite_12_Ft_Mound_FL, 16 Plexaura_homomalla_in_hospite_San_Blas_Panama, 17 Pseudoterogorgia_elisabethae_culture_Bahamas, 18 Plexaura_kuna_in_hospite_Bahamas, 19 Plexaura_kuna_culture_#704_San_Blas_Panama, 20 Eunicea_sp_in_hospite_12_Ft_Mound_FL, 21 Plexaura_flexuosa_culture_Tennessee_Reef_FL, 22 Plexaura_kuna_culture_#702_San_Blas_Panama, 23 Symbiodinium_kawagutii, 24 Pseudoterogorgia_americana_in_hospite_FL; TREE Fig._3 = [&R] (23,(24,1,2,3,4,5,6,7,8,9,(11,16),12,13,14,15,17,18,19,20),((10,22),21)); TREE Unpublished_Figure = [&R] (23,24,(1,2,3,4,5,(6,9),7,8,11,12,18,19,22),10,(13,17),(14,21),15,16,20); END;