#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 July 09, 2025; 16:19 GMT TreeBASE (cc) 1994-2008 Study reference: Salvi D., Bellavia G., Cervelli M., & Mariottini P. 2010. The analysis of rRNA sequence-structure in phylogenetics: An application to the family Pectinidae (Mollusca: Bivalvia). Molecular Phylogenetics and Evolution, 56(3): 1059-1067 . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S13548] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=26; TAXLABELS Aequipecten_opercularis_1 Aequipecten_opercularis_2 Amusium_pleuronectes Argopecten_irradians_ Azumapecten_farreri Flexopecten_flexuosus Flexopecten_glaber_1 Flexopecten_glaber_2 Manupecten_pesfelis_1 Manupecten_pesfelis_2 Mimachlamys_nobilis Mimachlamys_varia_1 Mimachlamys_varia_2 Mizuhopecten_yessoensis Pecten_jacobaeus_1 Pecten_jacobaeus_2 Pecten_keppelianus_1 Pecten_keppelianus_2a Pecten_keppelianus_2b Pecten_maximus_1 Pecten_maximus_2 Pecten_novaezelandiae Semipallium_fulvicostata Spondylus_gaederopous Talochlamys_multistriata Talochlamys_pusio ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M14847] TITLE ITS2; LINK TAXA = Taxa; DIMENSIONS NCHAR=383; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Aequipecten_opercularis_1 AAAACATCTATCGCAA--CTGCATGCACATACA--GC------GTTGCGCCTTGGATCGTACAACTCCACGTACGCCGTATTTCGA----------------GACGGAAACGAGGAGCGATCCCAA-ATGCAA-----TCGTCCCATCTCATAAAAAGC---CTAACCGAGTAGTTCGGTGTTGAAATCGCCCGTTTAACGG-ACGA-CCGAGA--CGCAGCTCGAAT--ATTAATCAAGTGCGCTCG---------------ACTGTTCAAAAAACC-------------------TTTGTGTGGTG-TTATTT-TCATTGGCC-----------GATGAA-------------GACGTTAAAAAAAA-----ATCAAAACC Aequipecten_opercularis_2 AAAACATCTATCGCAA--CTGCATGCACATACA--GC------GTTGCGCCTTGGATCGTACAACTCCACGTACGCCGTATTTCGA----------------GACGGAAACGAGGAGCGATCCCAA-ATGCAA-----TCGTCCCATCTCATAAAAAGC---CTAACCGAGTAGTTCGGTGTTGAAATCGCCCGTTTAACGG-ACGA-CCGAGA--CGCAGCTCGAAT--ATTAATCAAGTGCGCTCG---------------ACTGTTCAAAAAACC-------------------TTTGTGTGGTG-TTATTT-TCATTGGCT-----------GATGAA-------------GACGTTAAAAAAAA-----ATCAAAACC Amusium_pleuronectes GAAACATCTATCGCAA--CGTTATGCACACATCAAGC------GTTGCGCCTTGGACCGTACTAACTCCGTGTCGATTGCGCGTTGT---------------CGTGGCA-CGCGGAGCGGTCCGAA-ATGTTGAC-GATCGGAGTAAATTTCACACA-------GACCGAGTAGTTCGGTGTTGAGATCGCCC--GCAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CATATCAA-GTGCGCTCG---------------ACTGTCTCGCGAATC---------------GAAGGGCCTTTTCAAGT-GAGACTCCGTGAAG------------------------------TCGTTTTTCAATCTT--TTTT-----TC Argopecten_irradians_ AGAATATCTATCGCAA--CTGCATGCACAT--GAAGC------GTTGCGCCTTGGACCGTACATCTCCACGTTTGTTTGCTTGAGA----------------AACGATA-CGAGGAGCGGTCTCAA-ATACACA---GTCGCATCATCGTTCGCCAAA----AAAACCGAGTAGTTCGGTGTTGAAATCGTCCGTGAAACGGAACGA-CCGAGA--CGCAGCTCGAAT-GATCAATCAAGTGCGCTCG---------------ACTGTTCCCGATGAA-------------------CATGTG-GGCA-TCATGG-T-ATCGGCG-----------ATGAGA-------------CTGACAAAAAAAACTC--TATCAAAAAC Azumapecten_farreri AAAACATCTATCGCAAC-CTGCATGCACAGCAG---C------ATTGCGCCTTGGACCG---------TCTCGTCTCCCCG-------------------------------GCGAGCGGTCTTAA-ATGAGGA---ATCAGAGTCTC-----CAATCG---AACCAAAAACAAACCAGTACG-------------GAACAAATT-A-C-AAGAGACGCAGTTCGATT-AA-ACACAAAATGCGCTCTCGGTTCC--GTGAA-ACTGTAG-GTTCGCCT--TTTACATGTGAA--AAAAAAGGT---A-TGATGGT---GTAAATTTCTCTGGTCGACACAA-------------CACTTTGTGTTTGTCT--TTTCACAC-- Flexopecten_flexuosus AAAACATCTATCGCAA--CTGCGTGC--ATACGAAGC------GTTGCGCCTTGGACCGTATATCTCCTCGTCCGCCGT--TTTGT----------------GACGGCA-CGGGGAGCGGTCCCAA-ATGCA------TGTTTCCATC--ATAAAAG-----CCAACCGAGTAGTTCGGTGTTGAAATCGCCC-TTGAAGGG-ACGAACCGAGA--CGCAGCTCGAAT--AACAATCAAGTGCGCTCG---------------ACTGTTCCCGAA-----------------------------GGCG-TTTTTC-TGACAGGCG-----------ATGGAA-------------CACTTTGAA-----------TCAAAACC Flexopecten_glaber_1 AAAACATCTATCGCAA--CTGCGTGC--ATACGAAGC------GTTGCGCCTTGGACCGTACATCTCCTCGTCCGCCGT--TTTGT----------------GACGGCA-CGGGGAGCGGTCCCAA-ATGCA------TGTTTCCATC--ATAAAAG-----CCAACCGAGTAGTTCGGTGTTGAAATCGCCC-TTGAAGGG-ACGA-CCGAGA--CGCAGCTCGAAT--AACAATCAAGTGCGCTCG---------------ACTGTTCCCGAA-----------------------------GGCG-TTTTTC-TGACAGGCG-----------ATGGAA-------------CACTTTGAA-----------TCAAAACC Flexopecten_glaber_2 AAAACATCTATCGCAA--CTGCGTGC--ATACGAAGC------GTTGCGCCTTGGACCGTACATCTCCTCGTCCGCCGT--TTTGT----------------GACGGCA-CGGGGAGCGGTCCCAA-ATGCA------TGTTTCCATC--ATAAAAG-----CCAACCGAGTAGTTCGGTGTTGAAATCGCCC-TTGAAGGG-ACGA-CCGAGA--CGCAGCTCGAAT--AACAATCAAGTGCGCTCG---------------ACTGTTCCCGAA-----------------------------GGCG-TTTTTC-TGACAGGCG-----------ATGGAA-------------CACTTTGAA-----------TCAAAACC Manupecten_pesfelis_1 AAAACATCTATCGCAAA-CTGCATGCACATCAG---C------TTTGCGCCTTGGACCGGTTTTTACTGCCGTATTTGTTTATTTA----------------TAAGCAAAGAGGCAGCGGTCTTAAGAAAAAAA---GTCAGAGTCTC-----CAA------AATATTGAACGACATGTACAGCCCAGTGC----GGAACAAAAC-A-C-GAGAGACGCAGCTCGATA-GA--GATAAAATGCGCTGTCGGGTGT---TCCAAACTGAAATACGGGCC-------------------AACACATGAAC---AAACTGAAATGGTTTTTTTTTGGTGGTGTAA-------------TTCTCTGTCCTTAAAC-ATTTCTCACT- Manupecten_pesfelis_2 AAAACATCTATCGCAAA-CTGCATGCACATCAG---C------TTTGCGCCTTGGACCGGTTTTTACTGCCGTATTTGTTTATTTA----------------TAAGCAAAGAGGCAGCGGTCTTAAGAAAAAAA---GTCAGAGTCTC-----CAA------AATATTGAACGACATGTACAGCCCAGTGC----GGAACAAAAC-A-C-GAGAGACGCAGCTCGATA-GA--GATAAAATGCGCTGTCGGGTGT---TCCAAACTGAAATACGGGCC-------------------AACACATGAAC---AAACTGAAATGGTTTTTTTTTGGTGGTGTAA-------------TTCTCTGTCCTTAAAC-ATTTCTCACT- Mimachlamys_nobilis AAAACATCTATCGCAAA-CTGCGGGCACAGCAG---C------ATTGCGCCTTGGACCG---------TACATCTCATCTCCCCG--------------------------GGTGAGCGGTCCTAA-ATGACAA---ATCAGAGTCTC-----CAGGCA---AACGGTAAACACATCC-AGTA-------C----GGAACAAA---A-C--AGAGACGCAGCTCGGTTGC---TATGAATTGCGCTCC---------AAGTATCCGGGATTGTTGACC-----------TGAA----AATATGTTTGC-CAACTAGCAGGTGAATCAAAAATATTGACGAAA----------------TTTTTTTT--------CTCACTC-- Mimachlamys_varia_1 ATAACATCTATCGCAAA-CTGCATGCACAGCAG---C------GTTGCGCCTTGGGCCG---------TATACCTCTCATTGACT--------------------------TGGGAGCGGTCTCAA-ATGACGA---ATCAGAGTCTC-----CTAGCG---AATGCACGGGCAAACGAAATATCCAGTAT----GGGACATAAA-T-C-GAGAGACGCAGCTCGATG-CA--CATGAAATGCGCTCCCGGGTTCCGATAAGTACTGATC-GTTCTGTCAGTTCGCAAATAAAAGATCCAATGTGAAG-TGATCAAACGGTGTAATGCTCTGTTCGGCAGAA----------------TTAATTTTTTGCC--TTTCACAC-- Mimachlamys_varia_2 ATAACATCTATCGCAAA-CTGCATGCACAGCAG---C------GTTGCGCCTTGGGCCG---------TATACCTCTCATTGACT--------------------------TGGGAGCGGTCTCAA-ATGACGA---ATCAGAGTCTC-----CTAGCG---AATGCACGGGCAAACGAAAAATCCAGTAT----GGAACATAAA-T-C-GAGAGACGCAGCTCGATG-CA--CATGAAATGCGCTCCCGGGTTCCGATAAGTACTGATC-GTTCTGTCAGTTCGCAAATAAAAGATCCAATGTGAAG-TGATCAAACGGTGTAATGCTCTGTTCGGCAGAA----------------TTAATTTTTTGCC--TTTCACAC-- Mizuhopecten_yessoensis AAAACATCTATCGCAAA-CTGCATGCACGTCAG---C------GTTGCGCCTTGGACCG---------TACATCTCCTCCTTACTTA----------------------AGGGGGAGCGGTCTCAA-ATGATGA---ATCAGAGTCTC-----CAAGCG---AACGTAGCAAAAACCCCGGTAAA-AAAAC----GGAACATTTA-A-C--AGAGACGCAGCTCGATG-CA---CAAACATGCGCTCTCAGTTTCCAAAAAGAAAGGGGGCGTTCAAT----------ATGA------AAATGT---G-AGAAAAT---ATAAAAGCTT----TCGGCACGT-------------T-TTGTTTTACGAGCC--TTTCACAC-- Pecten_jacobaeus_1 AAAACATCTATCGCAA--CGGTATGCACATAAC--G--------TTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGAGGAGCGGTCCCAA-ATGTTTTCTGATCGGAGGTGCTTTTACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA-------------CCATTTATCGAAAATG--AATCAC--TT Pecten_jacobaeus_2 AAAACATCTATCGCAA--CGGTATGCACATAAC--G--------TTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGGGGAGCGGTCCCAA-ATGTTTTCTGATCGGAGGTGCTTTTACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA-------------CCATTTATCGAAAATG--AATCAC--TT Pecten_keppelianus_1 AAAACATCTATCGCAA--CGGTATGCACATAAC--GC------GTTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGGGGAGCGGTCCCAA-ATGTTACCTGATCGGAGGTGCTTT-ACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA------------------------AATTG--AATCAC--TT Pecten_keppelianus_2a AAAACATCTATCGCAA--CGGTATGCACATAAC--GC------GTTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGGGGAGCGGTCCCAA-ATGTTACCTGATCGGAGGTGCTTT-ACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA------------------------AATTG--AATCAC--TT Pecten_keppelianus_2b AAAACATCTATCGCAA--CGGTATGCACATAAC--GC------GTTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGAGGAGCGGTCCCAA-ATGTTACCTGATCGGAGGTGCTTT-ACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA------------------------AATTG--AATCAC--TT Pecten_maximus_1 AAAACATCTATCGCAA--CGGTATGCACATAAC--G--------TTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGAGGAGCGGTCCCAA-ATGTTTTCTGATCGGAGGTGCTTTTACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA-------------CCATTTATCGAAAATG--AATCAC--TT Pecten_maximus_2 AAAACATCTATCGCAA--CGGTATGCACATAAC--G--------TTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGTA-CGAGGAGCGGTCCCAA-ATGTTTTCTGATCGGAGGTGCTTTTACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--GGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA-------------CCATTTATCGAAAATG--AATCAC--TT Pecten_novaezelandiae AAAACATCTATCGCAA--CGGTATGCACATAAC--GC------GTTGCGCCTTGGGCCGTACAACTCCACGTCGATTGATTGTTTT----------------CATGGCA-CGAGGAGCGGTCCCAA-ATGTTACCTGATCGGAGGTGCTTT-ACGCACG---ACAACCGAGTAGTTCGGTGTTGAAATCGCCC--AGAACGGGACGA-CAGAGA--CGCAGCTCGAAT--CACATCAGTGTGCGCTCG---------------AATGTCACCGTCACT-------------------GACGTTTTCA-GTTGAGACTCCGTGAAG-----------GCCAAA-------------------------AT-G--AATCAC--TT Semipallium_fulvicostata AAAACATCTATCGCAAA-CTGCAGGCACGTCAG---C------TTTGCGCCTTGGACCGGTTT---CTGTCGCATTTGTC-GGTAG----------------TGACGAGAGCGGCAGCGGTCTTAAGAAAAAAA---GTCAGAGTCTC-----CAG------AACA--------CATGTTGTGCCCAGCGA----GAGACA-------------GACGCAGGTCGATT-T---GATTAAATGCGCTGTCTT---------TG-AC----ATACGGGGGCC-----------------AACAAATTAAC-TAAAAGTGAAAAAAGTT---------GGTGTAA-------------TTCTCTGGCACGAAACGAGTTCTTACTC Spondylus_gaederopous TGAATTTCCATCGCAGAGGCGTAGGCAAATGGCATGCCGCGCAACTGCGCCTTGGATCGAAAAACTTCCAACCCCCCCTTATTTGGGGGGTAGGGGAAGCGGTCCCAAGTTGAACAACGAACTTGCACTAACTGCTTTCGAGCGTTCGGGGTCTCGGCATATTTTGCCTCCGGCAACCGCAGTCGGAAAGTTGCCCGGGCGGGGCAGAC---GAGACGCAGGTCGGTG---ACAAAAACGTGCGCTCTC-------------GCCCGTCCATGAAAAA------------GGGTATACTCCCCGGGCTGTGCTCTGGGA-------------GCCGGCTGGTGGTCGAGATTTGTTCGACTCGCTCAAAGCA-TTTCTTTCTT Talochlamys_multistriata ATAACATCTATCGCAAA-CTGCATGTACAGCAG---C------GTTGCGCCTTGGGCCG---------TATAACTCTCGTGTGGTAA----------------------A-TGAGAGCGGTCTCAA-ATAACGA---ATCAGAGTCTC-----CGAGCG---AACGCAGTTTGAGACGAAATA--------------AATTCAGT-A-C-GAGAGACGCAGCTCGATT-TG-----TGAAATGCGCTCTCAC------ACATGTACTGTGATTTTCGTTGAGTTCGCCAATGA---ATCAAATGT----ATGAAAACTCGGTGTAATTCTCTGCTCGGCA-A-------------T---ATGATTGCCTT----TTCACAC-- Talochlamys_pusio ATAACATCTATCGCAAA-CTGCGTGTACAGCAG---C------GTTGCGCCTTGGGCCG---------TATAACTCTCGTGTGGTAA----------------------A-TGAGAGCGGTCTCAA-ATAACGA---ATCAGAGTCTC-----CGAGCG---AACGCAGTTTGAGACGAAATA--------------AATTCAGT-A-C-GAGAGACGCAGCTCGATT-TG-----TGAAATGCGCTCTCAT------ATATGTACTGTGATTT-CGTTGAGTTCGCCAATGA---ATCAAATGT----ATGAAAACTCGGTGTAATTCTCTGCTCGGCATA-------------T---ATAATTGCCTG----TTCACAC-- ; END;