#NEXUS [written Fri Apr 08 12:54:18 CDT 2011 by Mesquite version 2.72 (build 528) at swh223-01c1df/137.216.177.35] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=25; TAXLABELS Morus_rubra Morus_serrata Morus_cathayana Triphis_involucrata Morus_macroura Trophis_racemosa Morus_mongolica Morus_notabilis Morus_australis Morus_mesozygia Streblus_smithii Morus_insignis Morus_microphylla Morus_celtidifolia Streblus_banksii Streblus_heterophyllus Sorocea_affinis Sorocea_pileata Streblus_glaber Sorocea_muriculata Morus_nigra Morus_alba Milicia_excelsa Bagassa_guianensis Artocarpus_heterophyllus ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=666; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Morus_rubra TCGAAACCTGCAGAGCAGAAA-GACCAGCGGACCCATT-ACAACACCCAGGGG-CGACGTGCGCAATGCGCCC-CAACCCC-TGACGTCGAGTGTGTGCAG-----------CCCTGCCTTGCGCCCTCGG-CATAAAACGAACCCAGGCGCGGAACGCGTCAAGGAATCATAACGAAACGAGCTCCTGTTGTGGCCCCGGGGACGGTGATTGCCGCAGCGGCTGTGTTGTGCTTGGTTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATCAGGTTGAGGGCACGTCTGCCTGGGTGTCAAACACCGTTGCCCCCC-----AAATCCCC-TCGTCACTCTCCCC-TGAGTGCCCGGGGAGTGTGGGGGTCGGATGATGGCCTCCCGTGTGTCTTGGCTCGCGGTTGGCCCAAAGT-TGAGTCCTCGGTCACGGTTACCGTGGTGACAGGTGGTTGTCGGTCACTTGGTACCCCGTCACGTGCGCCGG-ACACGA--ATC--AAGACTCTCTTGATTA---CCCC-AACGCATCCC-GCGTGGGTGCTTCTGATGTGA Morus_serrata TCGAAACCTGCAAAGCAGAAA-GACCAGCGGACCCATT-ACAACACCCAGGGG-TGA-------------CCC-CAACCCC-TGACGCTGAGTGTGTGCAG-----------CCCTGCCTTGCGCCCTCAG-CATAAAACGAACCCAGGCGCGGAACGCGTCAAGGAATCATAACGAAACGAGCTCCTGCCGTGGCCCCGGGGACGGTGATCGCCGCAGCAGCTGTGTTGTGCTT-GGTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCAAACACCGATGCCCCCCC----AAATCCCC-TCGTCACTCTCCCC-TGAGTGCCCGGGGAGTGTGGGGGTCGGATGATGGCCTCCCGTG--TCTTGGCTCGCGGTTGGCCCAAAGT-CGAGTCCTCGGTCACGGTTACCGTGGTGACAGGTGGTTGTCGGTCGCTCGGTACCCCGTCACGTGCGCCGG-ACACGA--ATC--GAGACTCTCTTGATTA----CCCCAACGCATCCCCGTTTGGGTGCCTCTGATGTGA Morus_cathayana TCGAAACCTGCAAAGCAGAAA-GACCAGCGGACCCATT-ACAACACCCAGGGG-TGA-------------CCC-CAACCCC-TGACGCTGAGTGTGTGCGG-----------CCCTGCCTTGCGCCCTCAG-CATAAAACGAACCCAGGCGCGGAACGCGTCAAGGAATCATAACGAAACGAGCTCCTGCCGTGGCCCCGGGGACGGTGATCGCCGCAGCAGCTGTGTTGTGCTT-GGTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCAAACACCGATGCCCCCCC----AAATCCCC-TCGTCACTCTCCCC-TGAGTGCCCGGGGAGTGTGGGGGTCGGATGATGGCCTCCCGTG--TCTTGGCTCGCGGTTGGCCCAAAGT-CGAGTCCTCGGTCACGGTTACCGTGGTGACAGGTGGTTGTCGGTCGCTCGGTACCCCGTCACGTGCGCCGG-ACACGA--ATC--GAGACTCTCTTGATTA----CCCCAACGCATCCCCGTGTGGGTGCCTCTGATGTGA Triphis_involucrata TCGAAACCTGCGAAGCAGAAA-GACCTGCGAACCCGTT-ACAACACTC-GGGGGCGATGTGCGCAACGCGCCT-CGACCCC-TGACGCTGAGTGCGTGCAG-----------CCCTGCCTCGCGCCCTCGG-CATCAAACGAACCCAGGCGCGGAACGCGTCAAGGAAACACAACGAAACGAGCTCCTGCCGTGGCCCCGGGGACGGTGCTCGCCGCGGCGGCTGTGTCGTGCTTGGTTTAAGTCTATAA-CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGTGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATCAGGCTGAGGGCACGTCTGCTTGGGCGTCAAACACCGTTGCCCCCCC----AAATCCCC-TCGTCACTCTCCCC-TGAGTGCCCAGGTAGTGTGGGGGGCGGATGATGGCCTCCCGTGCGTCCTGGCTCGCGGTTGGCCCAAAGT-TGAGTCATCGGTCACGGTTGCCGTGGCAACAGGTGGTTGTCGGTTGCTCGGTGCCCCGTCACGTGCGCCGG-ACACGA--AAT--GAGACTCTCTTGTCTATAACCCCCAACGCATCCT-GCATGGGTGCTTTTGACGCGA Morus_macroura TCGAAACCTGCAAAGCAGAAA-GACCAGCGGACCCATT-ACAACACCCAGGGG-TGA-------------CCC-CAACCCC-TGACGCTGAGTGTGTGCGG-----------CCCTGCCTTGCGCCCTCAG-CATAAAACGAACCCAGGCGCGGAACGCGTCAAGGAATCATAACGAAACGAGCTCCTGCCGTGGCCCCGGGGACGGTGATCGCCGCAGCAGCTGTGTTGTGCTT-GGTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCAAACACCGATGCCCCCCC----AAATCCCC-TCGTCACTCTCCCC-TGAGTGCCCGGGGAGTGTGGGGGTCGGATGATGGCCTCCCGTG--TCTTGGCTCGCGGTTGGCCCAAAGT-CGAGTCCTCGGTCACGGTTACCGTGGTGACAGGTGGTTGTCGGTCGCTCGGTACCCCGTCACGTGCGCCGG-ACACGA--ATC--GAGACTCTCTTGATTA----CCCCAACGCATCCCCGTGTGGGTGCCTCTGATGTGA Trophis_racemosa TCGAAACCTGCAAAGCAGAAA-GACCCGTGAACCCTTT-ACAACACTC-GGGGGCGATGCGCGCAACGCGCCT-CGACCCC-TGACGCTGAGTGCGTGCAG-----------GCCTGCCTCGCGCCCTTAG-CATCAAACGAACTCAGGCGCGGAACGCGTCAAGGAAACATAACGAAACGATCTCCTGCCGTGGCCCCGGGGACGGTGCTCGCCGCGGCGGCTGTGTCGTGCTTGGTTTAAGTCTATAA-CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGTGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATCAGGCTAAGGGCACGTCTGCTTGGGCGTCAAACACCGTTGCCCCCCCTCCCAAATCCCC-TTGTCACTCTCCCC-TGAGTGCCCGGGTAGTGT---GGGCGGATGATGGCCTCCCGTGCGTCCTGGCTCGCGGTTGGCCCAAAGT-TGAGTCATCGGTCGCGGTTGCCGTGGCAACAGGTGGTTGTCGATTGCTCGGTGCCCCGTCACGTGCGCCGG-ACACGA--ACT--GAGACTCTCTTGTCTATAAAACCCAACGCATCCT-GCATGGGTGCTTTTGACGCGA Morus_mongolica TCGAAACCTGCAAAGCAGAAA-GACCAGCGGACCCATT-ACAACACCCAGGGG-TGA-------------CCC-CAACCCC-TGACGCTGAGTGTGTGCAG-----------CCCTGCCTTGCGCCCTCAG-CATAAAACGAACCCAGGCGCGGAACGCGTCAAGGAATCATAACGAAACGAGCTCCTGCCGTGGCCCCGGGGACGGTGATCGCCGCAGCAGCTGTGTTGTGCTT-GGTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCAAACACCGATGCCCCCCC----AAATCCCC-TCGTCACTCTCCCC-TGAGTGCCCGGGGAGTGTGGGGGTCGGATGATGGCCTCCCGTG--TCTTGGCTCGCGGTTGGCCCAAAGT-CGAGTCCTCGGTCACGGTTACCGTGGTGACAGGTGGTTGTCGGTCGCTCGGTACCCCGTCACGTGCGCCGG-ACACGA--ATC--GAGACTCTCTTGATTA----CCCCAACGCATCCCCGTTTGGGTGCCTCTGATGTGA Morus_notabilis TCGAAACCTGCAAAGCAGAAA-GACCAGCGGACCCATT-ACAACACCCAGGGG-TGA-------------CCC-CAACCCC-TGACGCTGAGTGTGTGCAG-----------CCCTGCCTTGCGCCCTCAG-CATAAAACGAACCCAGGCGCGGAACGCGTCAAGGAATCATAACGAAACGAGCTCCTGCCGTGGCCCCGGGGACGGTGATCGCCGCAGCAGCTGTGTTGTGCTAAGGTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCAAACACCGATGCCCCCCC----AAATCCCC-TCGTCACTCTCCCC-TGAGTGCCCGGGGAGTGTGGGGGTCGGATGATGGCCTCCCGTG--TCTTGGCTCGCGGTTGGCCCAAAGT-CGAGTCCTCGGTCACGGTTACCGTGGTGACAGGTGGTTGTCGGTCGCTCGGTACCCCGTCACGTGCGCCGG-ACACGA--ATC--GAGACTCTCTTGATTA----CCCCAACGCATCCCCGTGTGGGTGCCTCTGATGTGA Morus_australis TCGAAACCTGCAAAGCAGAAA-GACCAGCGGACCCATT-ACAACACCCAGGGG-TGA-------------CCC-CAACCCC-TGACGCTGAGTGTGTGCAG-----------CCCTGCCTTGCGCCCTCAG-CATAAAACGAACCCAGGCGCGGAACGCGTCAAGGAATCATAACGAAACGAGCTCCTGCCGTGGCCCCGGGGACGGTGATCGCCGCAGCAGCTGTGTTGTGCTAAGGTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCAAACACCGATGCCCCCCC----AAATCCCC-TCGTCACTCTCCCC-TGAGTGCCCGGGGAGTGTGGGGGTCGGATGATGGCCTCCCGTG--TCTTGGCTCGCGGTTGGCCCAAAGT-CGAGTCCTCGGTCACGGTTACCGTGGTGACAGGTGGTTGTCGGTCGCTCGGTACCCCGTCACGTGCGCCGG-ACACGA--ATC--GAGACTCTCTTGATTA----CCCCAACGCATCCCCGTTTGGGTGCCTCTGATGTGA Morus_mesozygia TCGAAACCTGCAAAGCAGAAA-GACCTGTGAACACGTT-ACAACACT--GGGGGTGATGTGCGCAATGCG-CTCCGACCCCCCGACGCTGAGTGCGTGCAG-----------CCCTGCCTCGCGCCCTTTG-CATCAAACGAACCCCGGCGCGGAATGCGTCAAGGAAACACAACAAAACGAGCTGACGTCGCGGCCCCGGGGACGGTGTTTGCCGTGGCGACTGTGTCGTGCTTAGTTTAAGTCTAAAA-CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCAAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCACACACCGTTGCCCCCC----AAAATCCCT----------------TGATTGCTCAGGGAGTGT-GGGGGCGGAAGGTGGCCTCCCGTGCGTGCTGGTTCGCGGTTGGCC-AAAATTTGAGTCCTCGGTCACGGCTGCCGTGGCAACAGGTGGTTGTCGATCACTCGGTGCCCCGTCACGTGCGCTGG-ACACGA--ACC--GGGACTC--TTGTTGA----CCCCGACGCATCCC-ACGAGGGTGCTTCCAACGCGA Streblus_smithii TCGAAACCTGCAAAGCAGAAA--ACCCGTGAACCCGTT-ACAACAAC--GGGGGTGATGTGCGTAACGCGCCC-TAACCCT-CGACGCCGAGTGCGTACGG-----------CCCCGCCTCGCGCCCTCGG-CATCAAACGAACCCCGGCGCGGAATGCGTCAAGGAAACACAACGAAACGAGCTCCCGTCGCGGCCCCGGAGACGGTGCTTGCCGCGGCGGCTGTGTCGTGCTTAGTTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCAAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCACACACCGTTGCCCCCCC---AATATCCCC-TCGTGACTCTCCCC-CGAGTGCCCGGGGATTGTGGGGGGCGGACGATGGCCTCCCGTGCGTCCTGGATCGCGGTTGGCCCAAAGT-CGAGTCCTCGGTCACGGTTGCCGTGGCAAAAGGTGGTTGTCGGTCACTCGGTGCCCCGTCACGTGCGCCGG-ACGCGA--ACC--GAGACTC--TTGTCTA----CCCCAATGCATCCC-GTGCTGGTGCTTCCGACGCGA Morus_insignis TCGAAACCTGCAGAGCATAAAAGACCCGCGAACCCGTT-ACAACACC--GGGGGTGATGTGCGCAATGCG-CTCCGACCCC-CGACGCCGAGTGCGTGCGG-----------CTCCGCCCCACGCCCTCGG-CATCAAACGAACCCCGGCGCGGAACGCGTCAAGGAAACACAACGAAACGAGCTCCCACCGCGGCCCCGGGGACGGTGCTTGCCGCGGTGGCTGTGTCGTGCTTATTTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCAAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCACACACCGTTGCCCCCC----AAAATCCCCTTGTCACTCTCCCC--CGAGTGCCCGGGGAGTGCGGGGGGCGGATGATGGCTTCCCGTGCGTCATGGCTCGCGGTTGGCCCAAAGT-TGAGTCCTCGGTCACGGTTGCCGTGGCAACAGGTGGTTGTCGGTCACTCGGTGCCCCGTCACTTGCGCCGG-ACACGA--ATC--GAGACTC--TTGTCTA----CCCCAAAGCATCCC-GCGCGGGTGCTTCCGACGCGA Morus_microphylla TCGAAACCTGCAAAGCAGAAA-GACCAGCGGACCCATT-ACAACACCCAGGGG-CGACGTGCGCAATGCGCCC-CAACCCC-TGACTTCGAGTGTGTGCAG-----------CCCTGCCTTGCGCCCTCGG-AATAAA-CGAACCCAGGCGCGGAACGCGTCAAGGAATCATAACGAAACGAGCTCCTGTTGTGGCCCCGGGGACGGTGATCGTCACAGCGGCTGTGTTGTGCTTGGTTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCAAACACCGTTGCCCCCCC----AAATCCCC-TCGTCACTCTCCCC-TGAGTGCCCGGGGAGTGTGGGGGTCGAATGATGGCCTCCCGTGTGTCTTGGCTCGCGGTTGGCCCAAAGT-TGAGTCCTCGGTCACGGTTACCGTGGTGACAGGTGGTTGTCGGTCACTCGGTGCCCCGTCACGTGCGCCGG-ACACAA--ATC--GAGACTCTCTTGATTA---CCCCCAACGCATCCC-GCGTGGGTGCTTCTGATGTGA Morus_celtidifolia TCGAAACCTGCAAAGCAGAAA-GACCAGCGGACCCATT-ACAACACCCAGGGG-CGACGTGCGCAATGCGCCC-CAACCCC-TGACTCCGAGTGTGTGCAG-----------CCCTGCCTTGCGCCCTCGG-AATAAA-CGAACCCAGGCGCGGAACGCGTCAAGGAATCATAACGAAACGAGCTCCTGTTGTGGCCCCGGGGACGGTGATCGTCACAGCGGCTGTGTTGTGCTTGGTTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCAAACACCGTTGCCCCCCC----AAATCCCC-TCGTCACTCTCCCC-TGAGTGCCCGGGGAGTGTGGGGGTCGAATGATGGCCTCCCGTGTGTCTTGGCTCGCGGTTGGCCCAAAGT-TGAGTCCTCGGTCACGGTTACCGTGGTGACAGGTGGTTGTCGGTCACTCGGTGCCCCGTCACGTGCGCCGG-ACACAA--ATC--GAGACTCTCTTGATTA---CCCCCAACGCATCCC-GCGTGGGTGCTTCTGATGTGA Streblus_banksii TCGAAACCTGCAAAGCAGAAA-GACCCGTGAACCCGTT-ACAACAAC--GGGGGTGATGTGCGTAATGCGCCC-CAACCCT-CGACGCCGAGTGCGTACGG-----------CCCCGCCTCGCGCCCTCGG-CATCAAACGAACCCCGGCGCGGAATGCGTCAAGGAAACACAACGAAACGAGCTCCCGTCGCGGCCCCGGGGACGGTGCTTGCCGCGGCGGCTGTGTCGTGCTTAGTTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCAAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCACACACCGTTGCCCCCCC---AATATCCCC-TCGTGACTCTCCCC-TGAGTGCCTGGGGAGTGTGGGGGGCGGACGATGGCCTCCCGTGCGTCCTGGATCGCGGTTGGCCCAAAGT-CGAGTCCTCGGTCACGGTTGCCGTGGCAACAGGTGGTTGTCGGTCACTCGGTGCCCCGTCACGTGCGCCGG-ACGCGA--ACC--GAGACTC--TTGTCTA----CCCCAATGCATCCC-GTGCTGGTGCTTCCGACGCGA Streblus_heterophyllus TCGAAACCTGCAAAGCAGAAA-GACCCGTGAACCCGTT-ACAACAAC--GGGGGTGATGTGCGTAACGCGCCC-CAACCCT-CGACGCCGAGTGCGTACGG-----------CCCCGCCTCGCGCCCTCGG-CATCAAACGAACCCCGGCGCGGAATGCGTCAAGGAAACACAACGAAACGAGCTCCCGTCGYGGCCCCGGAGACGGTGCTTGCCGCGGCGGCTGTGTCGTGCTTAGTTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCAAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCACACACCGTTGCCCCCCC---AATATCCCC-TCGTTACTCTCCCC-CGAGTGCCCGGGGAGTGTGGGGGGCGGACGATGGCCTCCCGTGCGTCYTGGATCGCGGTTGGCCCAAAGT-CGAGTCCTCGGTCACGGTTGCCGTGGCAACAGGTGGTTGTCGGTCACTCGGTGCCCCGTCACGTGCGCCGG-ACGCGA--ACC--GAGACTC--TTGTCTA----CCCCAATGCATCCC-ATGCTGGTGCTTCCGA????? Sorocea_affinis TCAAAACCTGCAAAGAAGAAA-GACCGGCGAACCCGTT-ACAACACTC-GGGGGTGATGTGCGCAACGCTCCT-CAACCCC-TGGCGCCGAGTGCGTGTAGTTGCGTGCAGTGCC-GCCTCGCGCCCTCGG-CAATAAACGCACCCCGGCGCGAAACGCGTCAAGGAAACACAATGAAACGAGCTCCCGCCGCGGCCCCTGAAACGGGGCTTGCCGCGGGGGCTGTGTCGTGCCTGGTTTAAGTCTAAAA-CGACTCTCGGCAACGGATATTTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCTTCAGGCTGAGGGCACGTCTGCCTGGGCGTCACACACTGTTGCCCCCCCCC-AAAA-CCCCCTTATCGCTCTCCCC-CGAGTGTCGGGGGCGTGTGGGGGGCGGATGATGGCCTCCCGTGCGTCTTGGCTCGCGGTTGGCCCAAAGT-CGATTCCTCGGTCACGGTTGCCGTGGCAATAGGTGGTTGTCAACCACTCTGTGCCCCGTCATGCGCGCCGG-ACACAG--ACC--GAGACTC--TAGTCTA----CCCCAATGCATCCC-GCGTGGGTGCTTCTGACGCGA Sorocea_pileata TCAAAACCTGCAAAGAAGAAA-GACCGGTGAACCCGTT-ACAACACTC-GGGGGTGATGTGCGAAACGCTCCT-CAACCCT-TGACGCCGAGTGCGTGCAGTTGCGTGCAGTGCC-GCCTCGCGCCCTCGG-CAATAAACGCACCCCGGCGCGGAACGCGTCAAGGAAACACAATGAAACGAGCTCCCGCCGCGGCCCCTGAAATGGTGCTTGCCGCGGTGGCTGTGTCGTGCCTGGTTTAAGTCTAAAA-CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATTAATAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCTTCAGGCTGAGGGCACGTCTGCCTGGGCGTCACACACTGTTGCCCCCCTCCAAAAA-CCCC-TTATCGCTCTCCCC-CGAGTGTCGGGGGCGTGTGGGGGGCGGATGATGGCCTCCCGTGTGTCTTGGCTCGCGGTTGGCCCAAAGT-CGATTCCTTGGTCACGGTTGCCGTGGCAATAGGTGGTTGTCAACCACTCTGTGCCCTGTCATGCGCGCCGA-ACACAG--ACC--GAGACTC--TAGTCTA----CCCCAATGCATCCC-GCGCGGGTGCTTCTAACGCGA Streblus_glaber TCGAAACCTGCAAAGCAGAAA-GACCCGTGAACCCGTT-ACAACACC--GGGGGTGAAGTGCGCTACGCGCCC-CAACCCC-CGTCGCCGAGTGCGTGCGG-----------CCCCGCCTCGCGCCCTCGG-CATCAAACGAACCCCGGCGCGGAACGCGTCAAGGAAACACAACGAAACGAACTCCCGCTGCGGCCCCGGGGACGGTGCTTGCCGCGGCGGCTGTGTCGTGCTTAGTTTAAGTCTAAAA-CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCAAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCACACACCGTTGCCCCCCC--TAAAATCCCC-TCGTCACTCTTCCA-CGAGWGCCCGGGGAGTGTGGGGGGCGGATGATGGCCTCCCGTGTGTCCTGGCTCGCGGTTGGCCCAAAGT-CGAGTCCTCGGTCACGGTTGCCGTGGCAACAGGTGGTTGTCGGTCACTCGGTGCCCCGTCACGTGCKCCGG-ACACGA--ACC--GAGACTC--TTGTCTA----CCCCAATGCATCCC-GAGCGGGTGCTTCCGA????? Sorocea_muriculata TCAATACCTGCAAAGAAGAAA-GACCGGTGAACCCGTT-ACAACACTC-GGGGGTGATGTGCGAAACGCTCCT-CAGCCCC-TGGCGTCGAGTGCGTGTAGTTGCGTGCAATGCC-GACTCGCGCCCTCGG-CAATAAACGAACCCCGGCGCGGAATGCGTCAAGGAAACACAATGAAACGAGCTCCCGCCGCGGCCCCCGAAACGGTGATTGCCGCGGTGGTTGTGTCGTGCCTGGTTTAAGTCTAAAA-CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCTTCAGGCTGAGGGCACGTCTGCCTGGGCGTCACACACTGTTGCCCCCCCCCAAAAA-CCCC-ATATCGCTCTCCCC-TGAGTGCCAGGGGCGTGTGGGGGGCGGATGATGGCCTCCCGTGTGTCTTGGCTCGCGGTTGGCCCAAAGT-CGATTCCTCGGTCACGGTTGCCGTGGCAATAGGTGGTTGTCGACCACTCTGTGCCCTGTCATGCGCGCCGT-ACA--G--ACT--GAGACTC--TAGTCTA----CCCCAATGCAACCC-GCGTGGGTGCTTCTGACGCGA Morus_nigra TCGAAACCTGCAAAGCAGAAA-GACCAGCGGACCCATT-ACAACACCCAGGGG-TGA-------------CCC-CAACCCC-TGACGCTGAGTGTGTGCAG-----------CCCTGCCTTGCGCCCTCAG-CATAAAACGAACCCAGGCGCGGAACGCGTCAAGGAATCATAACGAAACGAGCTCCTGCCGTGGCCCCGGGGACGGTGATCGCCGCAGCAGCTGTGTTGTGCTT-GGTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCAAACACCGATGCCCCCCC----AAATCCCC-TCGTCACTCTCCCC-TGAGTGCCCGGGGAGTGTGGGGGTCGGATGATGGCCTCCCGTG--TCTTGGCTCGCGGTTGGCCCAAAGT-CGAGTCCTCGGTCACGGTTACCGTGGTGACAGGTGGTTGTCGGTCGCTCGGTACCCCGTCACGTGCGCCGG-ACACGA--ATC--GAGACTCTCTTGATTA----CCCCAACGCATCCCCGTTTGGGTGCCTCTGATGTGA Morus_alba TCGAAACCTGCAAAGCAGAAA-GACCAGCGGACCCATT-ACAACACCCAGGGG-TGA-------------CCC-CAACCCC-TGACGCTGAGTGTGTGCAG-----------CCCTGCCTTGCGCCCTCAG-CATAAAACGAACCCAGGCGCGGAACGCGTCAAGGAATCATAACGAAACGAGCTCCTGCCGTGGCCCCGGGGACGGTGATCGCCGCAGCAGCTGTGTTGTGCTT-GGTTAAGTCTAAAA-TGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCTGAAGCCATCAGGCTGAGGGCACGTCTGCCTGGGCGTCAAACACCGATGCCCCCCC----AAATCCCC-TCGTCACTCTCCCC-TGAGTGCCCGGGGAGTGTGGGGGTCGGATGATGGCCTCCCGTG--TCTTGGCTCGCGGTTGGCCCAAAGT-CGAGTCCTCGGTCACGGTTACCGTGGTGACAGGTGGTTGTCGGTCGCTCGGTACCCCGTCACGTGCGCCGG-ACACGA--ATC--GAGACTCTCTTGATTA----CCCCAACGCATCCCCGTTTGGGTGCCTCTGATGTGA Milicia_excelsa ?????????????????????????????GAATCTGTT-ACA-CACC--GAGGGAATTGTGTGCAATGCGCCCT-AACCCC-TGACATTGAGCACGTGTGG-----------CCCTGCGTCATG-CCCTTGACATCAAAACAAA-CTGGCGCAGAACGCGTCAAGGAAACACAATGAAAAGAGCTCCCGATGTGGCCCTAGG-ACGGTGCTTGCAGTAGTGGTTTCATCATGCTTAGTTTAAGTCCAAAA-TGACTCTCGGCAACGGATATCTCGACTCTCGCATCAATGAAGAATGTAACAAAACGCGATA-TTGGTGTGAATTGTAGAATCCT-GTGAACCATCGAG-----------------------------------------------------------------------------------------------------------AGTGCTCAGGGAGTGTGGGGG-TGGATGATGGCCTCCCATGTATCCTGGCTTGCAGTTGGCCCAAAGT-TGAGTCCTCAATCACGATTGCCAGGGCATCAGGTGGTTGTCGGTCACTTAGTGCCCCATCATGTGTGCTGG-ACACAA--A-CT-GAGACTC--TTGTTTA----CCTGAATGCATCCCG-TGTAGGT--TTTTGATGTGA Bagassa_guianensis ?????????????????????????????????????????????????????????????????????????????CCCC-CA?CGCC-AGCGCGCGCGG-----------CCCCGCCTCGC?CCCTCGG-CATCAAATGAACCCCGGCGCGGAACG?GTCAAGGAAAC?C-A?CAAACGATCTCCCGCCGTGGCCCCGGAGACGGTGCTAGCCGCGGCGGCTATGTCGTGCTTGGTATAAGTCTAAA?-CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCC-GTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCGTCAGGCTGAGGGCACGTCT?CCTGGGCGTCACACACTGTTGTCCCCCCC-ACAAATCCCC-TCGTCACTCTCCCC-CGAGTGCCCGGGGAGCGTGGGGGGCGGATGATGGCCTCCCGTGAGCCTTAGCTCGCGG?TGGCCCAAAGT-TGAGTCCTCGGTCACGGTTGCCGTGGCAAAAGGTGGTTGTCCGTCACTCGGTGCCCCGTCGCGCGCGCCGGTATCCAA???????????????????????----???????????????????????????????????? Artocarpus_heterophyllus TCGAAAC-TGCCCAGCAGAAA-GACCCGCGAACAGGTTTACAACACTT-GGGGGCGAGGGGTGCAACGCGCCTTGAACCCC-CCATGCCGAGYGCGTGTGG-----------CTTTGCCATGCGTCCCCGGCCACTAA-CCAACCCCGGCGCGGAATGCGTCAAGGAAACATAAAGAAACGAGCTTCTACTGTGGCCCCAGATTTGGTGCCTGCTGCAGCAGATGTGTCGTGTTTCG-TTAAGTCTAAAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATAATTGGTGTGAATTKMMGAATCCCCTGTAACCACSGAGTYTTTGAACGCAAGTTGCGCCCGAAGCCATCCGGTCGAGGGCACGTCTGCCTGGGCGTCACACACCGTTGCCCCCC----TAAGTCCC-TTTGACACTATCCATGTG-GTGCATGGGGACTACGAGTGGCGGATGATGGCCTCCCGTGGGCCTTGACTCGCGGTTGGTCTAAATT-TGAGTCCTCGGTCACGGTCRCCGTGGCAATAGGTGGTCGTCGATCATTCGGTGCCCTGCCACGTGCTCCGGGACAAAAGCATCGAGAGACTTTACAAACTT--GACCCCGATGCACCACAACGTAGGTGCTYCMAACGCGA ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 666; END; BEGIN TREES; Title 'Trees from "Figure 1a.tre"'; LINK Taxa = Taxa; TRANSLATE 1 Morus_rubra, 2 Morus_serrata, 3 Morus_cathayana, 4 Triphis_involucrata, 5 Morus_macroura, 6 Trophis_racemosa, 7 Morus_mongolica, 8 Morus_notabilis, 9 Morus_australis, 10 Morus_mesozygia, 11 Streblus_smithii, 12 Morus_insignis, 13 Morus_microphylla, 14 Morus_celtidifolia, 15 Streblus_banksii, 16 Streblus_heterophyllus, 17 Sorocea_affinis, 18 Sorocea_pileata, 19 Streblus_glaber, 20 Sorocea_muriculata, 21 Morus_nigra, 22 Morus_alba, 23 Milicia_excelsa, 24 Bagassa_guianensis, 25 Artocarpus_heterophyllus; TREE Strict_Consensus_of_8_MP_trees = ((((((1,(13,14)),(2,(3,5),7,(8,9),21,22)),(4,6)),(((10,23),12),(((11,16),15),19)),(17,(18,20))),24),25); TREE Figure_1_left = ((((((1,(13,14)),(2,(3,5),7,(8,9),21,22)),(4,6)),(((10,23),12),(((11,16),15),19)),(17,(18,20))),24),25); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 666; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 666; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1302285259004; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6178968109170687877; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5480536308773509804; checksumv 0 2 3553688022 null getNumChars 666 numChars 666 getNumTaxa 25 numTaxa 25 short true bits 2305843009213693967 states 15 sumSquaresStatesOnly 289859.0 sumSquares -5.995191823955601E19 NumFiles 1 NumMatrices 1; endTell; getWindow; tell It; suppress; setResourcesState false false 231; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1680 932; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #6178968109170687877 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #6178968109170687877; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1449 865; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.ManageTrees.ManageTrees; tell It; showTrees 0 #mesquite.lists.TreesList.TreesList; tell It; setTreeBlock 1; getWindow; tell It; newAssistant #mesquite.lists.NumForTreeList.NumForTreeList; tell It; suppress; setValueTask #mesquite.trees.NumberOfTaxa.NumberOfTaxa; desuppress; endTell; newAssistant #mesquite.lists.TreeListRooted.TreeListRooted; newAssistant #mesquite.lists.TreeListPolys.TreeListPolys; newAssistant #mesquite.lists.TreeListPolyAssumption.TreeListPolyAssumption; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1449 865; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TreesList.TreesListWindow.ibeam; endTell; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #6178968109170687877 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 807.1302284701433.566999428383436001; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1449 865; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientRight; setCornerMode Right_Angle 50; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 2; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #5480536308773509804 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1449 865; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; showCharacters #5480536308773509804 #mesquite.lists.CharacterList.CharacterList; tell It; setData 0; getWindow; tell It; newAssistant #mesquite.lists.CharListInclusion.CharListInclusion; newAssistant #mesquite.stochchar.CharListProbModels.CharListProbModels; newAssistant #mesquite.lists.CharListCodonPos.CharListCodonPos; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1449 865; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.CharListAnnotPanel.CharListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; endTell; end;