#NEXUS [written Tue Sep 02 15:23:06 EEST 2014 by Mesquite version 2.75 (build 564) at kostas-PC/192.168.1.92] BEGIN TAXA; TITLE Taxa_ITS1; DIMENSIONS NTAX=52; TAXLABELS Lecane_bulla Brachionus_bidentatus Brachionus_forficula Brachionus_diversicornis Brachionus_angularis_1 Brachionus_angularis_2 Brachionus_angularis_3 Plationus_patulus Brachionus_dimidiatus_3 Brachionus_dimidiatus_1 Brachionus_dimidiatus_2 Brachionus_manjavacas_1 Brachionus_manjavacas_2 Brachionus_sp._Austria_1 Brachionus_sp._Austria_2 Brachionus_sp._Austria_3 Brachionus_sp._Nevada_1 Brachionus_plicatilis_1 Brachionus_plicatilis_2 Brachionus_plicatilis_3 Brachionus_plicatilis_4 Brachionus_rotundiformis_1 Brachionus_rotundiformis_2 Brachionus_sp._Tiscar_1 Brachionus_sp._Tiscar_2 Brachionus_sp._Cayman_1 Brachionus_sp._Cayman_2 Brachionus_ibericus_1 Brachionus_ibericus_2 Brachionus_ibericus_3 Brachionus_ibericus_4 Brachionus_sp._Almenara_1 Brachionus_sp._Almenara_2 Brachionus_calyciflorus_1 Brachionus_calyciflorus_2 Brachionus_calyciflorus_3 Brachionus_calyciflorus_4 Brachionus_calyciflorus_5 Brachionus_sessilis_Doirani_1 Brachionus_sessilis_Doirani_2 Brachionus_sessilis_Doirani_3 Brachionus_sessilis_Doirani_4 Brachionus_sessilis_Doirani_5 Brachionus_sessilis_Balaton_1 Brachionus_sessilis_Balaton_2 Brachionus_rubens_1 Brachionus_rubens_2 Brachionus_rubens_3 Brachionus_urceolaris Brachionus_leydigii Brachionus_quadridentatus_1 Brachionus_quadridentatus_2 ; END; BEGIN CHARACTERS; TITLE DNA_alignment_of_ITS1; DIMENSIONS NCHAR=428; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = -; MATRIX Lecane_bulla CTTTATGCT-TTGTGCTATTTG-----CACAAAA-ATTAAAAAAACAGCTTAAAA---ATTTT-----------AAGTTGTA------------------ Brachionus_bidentatus CCTTTTGAA-TTGTGCTGCTTCAAAGCTCAACAATTTATTAAACA--------AACTCATCTT-----------TGACTATAGATACAT------TTTTT Brachionus_forficula CCTTTTGTG-TAGTGTGCACTG-------CATAC-TTACACTTTAGCATTTTACACACACTATG----------TATCTATAAATGCG-------TGTTT Brachionus_diversicornis CCTTTTGTG-TAGTGTGCACTG-------CATACTTGACACTTTAGCATTTTACACACACTATG----------TATCTATAAATGC--------TGTTT Brachionus_angularis_1 CCTTTGGTG-TAGTTTGCATTA---TGCATACTA--TACACTATAGCTTTTCACACACACTATG----------CATCTATAAATGC--------TGTTT Brachionus_angularis_2 CCTTTGGTG-TAGTTTGCATTA-----TGCATAC-TAACACTATAGCTTTTCACACACACTATG----------CATCTATAAATGCT-------TGTTT Brachionus_angularis_3 CCTTTGGTG-TAGTTTGCATTA-----TGCATAC-TAACACTATAGCTTTTCACACACACTATG----------CATCTATAAATGCT-------TGTTT Plationus_patulus CCTATTGCG-TAGTATCTTTTT----------AAATGCTACT----AGCTTAAAACACATGC------------AGGCTATGAATACT-------TGTTT Brachionus_dimidiatus_3 CCTTTTGCT-TAGAATTGTTAA------AAAACA-TTCTAAAGCATCAATAAATACACATTTT-----------GAGCTTTAAATGCT-------TGTTT Brachionus_dimidiatus_1 CCTTTTGCT-TAGAATTGTTAA------AAAACA-TTCTAAAGCATCAATAAATACACATTTT-----------GAGCTTTAAATGCT-------TGTTT Brachionus_dimidiatus_2 CCTTTTGCT-TAGAATTGTTAA------ACGACA-TTCTAAAGCATCAATTAATACACACTTT-----------GAGCTATAGATGCT-------TGTCT Brachionus_manjavacas_1 CTTTTTGCT-TAGATTTGCTAA-------CAAGCAATCTAAAGCATCATTTAAATCACACTTT-----------GAGTATTAGATGCT-------TGTCT Brachionus_manjavacas_2 CTTTTTGCT-TAGATTTGCTAA-----CAAGCAA--TCTAAAGCATCATTTAAATCACACTTT-----------GAGTATTAGATGCT-------TGTCT Brachionus_sp._Austria_1 CCTTTTGCT-TAGAACTGCTAA-------CAAGCATTCTAAAGCATCATTTAAATTACACTTT-----------GAGTTATAGATGCT-------TGTCT Brachionus_sp._Austria_2 CCTTTTGCT-TAGAACTGCTAA-------CAAGCATTCTAAAGCATCATTTAAATTACACTTT-----------GAGTTATAGATGCT-------TGTCT Brachionus_sp._Austria_3 CCTTTTGCT-TAGAACTGCTAA-------CAAGCATTCTAAAGCATCATTTAAATTACACTTT-----------GAGTTATAGATGCT-------TGTCT Brachionus_sp._Nevada_1 CCTTTTGCT-TAGAGCTGCTAA-------CAAGCATTCTAAAGCATTATTTAAATTACACTTT-----------GAGTTATAGATGCT-------TGTCT Brachionus_plicatilis_1 CCTTTTGCT-TAGAGCTGCTAA------CAAGCA-TTCTAAAGCATCATTTAAATTACACTTT-----------GAGTAATAGATGCT-------TGTCT Brachionus_plicatilis_2 CCTTTTGCT-TAGAGCTGCTAA-------CAAGCATTCTAAAGCATTATTTAAATTACACTTT-----------GAGTAATAGATGCT-------TGTCT Brachionus_plicatilis_3 CCTTTTGCT-TAGAGCTGCTAA------CAAGCA-TTCTAAAGCATTATTTAAATTACACTTT-----------GAGTAATAGATGCT-------TGTCT Brachionus_plicatilis_4 CCTTTTGCT-TAGAGCTGCTAA-------CAAGCATTCTAAAGCATTATTTAAATTACACTTT-----------GAGTAATAGATGCT-------TGTCT Brachionus_rotundiformis_1 CCTTTTGCT-TGGGATCGCTAA------ATACGA-TTCTAAAGCATTAATTAAATTACACTTT-----------GAGCTATAGATGCT-------TGTCT Brachionus_rotundiformis_2 CCTTTTGCT-TAGGATCGCTAA------ATACGA-TTCTATAGCATTAATTAAATTACACTTT-----------GAGCTATAGATGCT-------TGTCT Brachionus_sp._Tiscar_1 CCTTTTGCT-TAGAATTGTTAA------ATACAA-TTCAAAAGCATTAACTAAAATACACTTT-----------GAGCTTTAGATGCT-------TGTCT Brachionus_sp._Tiscar_2 CCTTTTGCT-TAGAATTGTTAA------ATACAA-TTCAAAAGCATTAACTAAAATACACTTT-----------GAGCTTTAGATGCT-------TGTCT Brachionus_sp._Cayman_1 CCTTTTGCT-AAGAATTGTTAA------ATACAA-TTCAAAAGCATCAACTAAAATACACTTT-----------GAACTTTAGATGCT-------TGTCT Brachionus_sp._Cayman_2 CCTTTTGCT-AAGAATTGTTAA------ATACAA-TTCAAAAGCATCAACTAAAATACACTTT-----------GAACTTTAGATGCT-------TGTCT Brachionus_ibericus_1 CCTTTTGCT-TAGAATTGCTAA------ATACAA-TTCTAAAGCATTAATTAAAATACACTTT-----------GAGCTTTAGATGCT-------TGTCT Brachionus_ibericus_2 CCTTTTGCT-TAGAATTGCTAA------ATACAA-TTCTAAAGCATTAATTAAAATACACTTT-----------GAGCTTTAGATGCT-------TGTCT Brachionus_ibericus_3 CCTTTTGCT-TAGAATTGCTAA------ATACAA-TTCTAAAGCATTAATTAAAATACACTTT-----------GAGCTTTAGATGCT-------TGTCT Brachionus_ibericus_4 CTTTTTGCT-TAGAATTGCTAA------ATACAA-TTCTAAAGCATTAATTAAAATACACTTT-----------GAGCTTTAGATGCT-------TGTCT Brachionus_sp._Almenara_1 CCTTTTGCT-TAGAATTGCTA-------AAACCAATTCTAAAGCATTAATTAAAATACACTTT-----------GAGCATTAGATGCT-------TGTCT Brachionus_sp._Almenara_2 CCTTTTGCT-TAGAATTGCTAA-------AACCAATTCTAAAGCATTAATTAAAATACACTTT-----------GAGCATTAGATGCT-------TGTCT Brachionus_calyciflorus_1 ----------------------------ATGCGA---TCACTCGCTAATTTAAAACACACTAT-----------GAGCTTTAGTTGCTAT-----TTTCT Brachionus_calyciflorus_2 CCTTTTGCGTTTGTGTCGCTGA------ATGCGA---TCACTCGCTAATTTAAAACACACTAT-----------GAGCTTTAGATGCTAT-----TTTCT Brachionus_calyciflorus_3 CCTTTTGCGTTTGTGTCGCTTA-------TGCGA---TCACTCGCTTATTTAAAACACACTTT-----------GAGTTTTAGATGCAAT-----TTTTT Brachionus_calyciflorus_4 CCTTTTGCGTTTGTGTCGCTAA-------TGCGA--TTCACTCGCTAATTTAAAACACACTAT-----------GAGTTTTAGATGCAT------CTTCT Brachionus_calyciflorus_5 CCTTTTGCGTTTGTGTCGCTTA-------TGCGA---TCACTCGCTAATTTAAAACACACTAT-----------GAGTTTTAGATGCTAT-----TTTCT Brachionus_sessilis_Doirani_1 CCTTTTGCG-TGGTATTCGTTGTTACTAACACGA-TACTACA--AACGCTTATAACTCACTAT-----------AGGTCATAAATACTGCATG--GTTTT Brachionus_sessilis_Doirani_2 CCTTTTGCG-TGGTATTCGTTGTTACTAACACGA-TACTACA--AACGCTTATAACTCACTAT-----------AGGTCATAAATACTGCATG--GTTTT Brachionus_sessilis_Doirani_3 CCTTTTGCG-TGGTATTCGTTGTTACTAACACGA-TACTACA--AACGCTTATAACTCACTAT-----------AGGTCATAAATACTGCATG--GTTTT Brachionus_sessilis_Doirani_4 CCTTTTGCG-TGGTATTCGTTGTTACTAACACGA-TACTACA--AACGCTTATAACTCACTAT-----------AGGTCATAAATACTGCATG--GTTTT Brachionus_sessilis_Doirani_5 CCTTTTGCG-TGGTATTCGTTGTTACTAACACGA-TACTACA--AACGCTTATAACTCACTAT-----------AGGTCATAAATACTGCATG--GTTTT Brachionus_sessilis_Balaton_1 CCTTTTGCG-TGGTATTCGTTGTTACTAACACGA-TACTACA--AACGCTTATAACTCACTAT-----------AGGTCATAAATACTGCATG--GTTTT Brachionus_sessilis_Balaton_2 CCTTTTGCG-TGGTATTCGTTGTTACTAACACGA-TACTACA--AACGCTTATAACTCACTAT-----------AGGTCATAAATACTGCATG--GTTTT Brachionus_rubens_1 CTTTTTGCG-TGGTATTCGTTG-TAAAAATACGA-TGCTACA--AACGCTTATAACTCACTATTAACTCAACTCGGGTCATAAATACTGC--TTGGTTTT Brachionus_rubens_2 CTTTTTGCG-TGGTATTCGTTG-TAAAAATACGA-TGCTACA--AACGCTTATAACTCACTATTAACTCAACTCGGGTCATAAATACTGCTTG--GTTTT Brachionus_rubens_3 CTTTTTGCG-TGGTATTCGTTT----TCATACGA-TGCTACA--AACGCTTATAACTCACTAG-----------AGGTCATAAATACTGCTTG--GTTTT Brachionus_urceolaris CCTTTAGCG-TAGTATCGCTTA------ATTCGA-TATTACA--AAGCTTTATAACACACTAT-----------TGGCTATTAAAACTGCTTTGTTTTTT Brachionus_leydigii CTTTTTGCG-TGGTATCGCATT------GTTCGA-TACTACA--AACGCTTAAAACACATTAA-----------TGGCCATAAATACTGCTATCAGTCTT Brachionus_quadridentatus_1 CTTTTTGCG-TGGTATTGTATA------GATCAA-TGCTACA--AACGCTTAAAACACACTAT------------GGCCATAAAAACTGCTATCGGTCTT Brachionus_quadridentatus_2 CTTTTTGCG-TGGTATTGTATA------GTTCAA-TGCTACA--AACGCTTAAAACACACTAT------------GGCCATAAAAGCTGCTATCGGTCTT Lecane_bulla ------------------------------AAATTCCATAT--TTGCATT---AATATG----GTCAGGTACCTTAGAA----------------AGCAA Brachionus_bidentatus ATAGTCATAGCTTT-----------------AAAATCATGCAAATTCTATCATAGTTTGACATGTCGGGTACCTACT----------------------- Brachionus_forficula ATAGATGCATGCTTGT---------AAAACAAAAATCATGC--ATGCTCGTATAGTATG-CATGTCGGGTACCTATT----------------------- Brachionus_diversicornis ATAGATGCATGCTTGT---------AAAACAAAAATCATGC--ATGCTCGTATAGTATGACATGTCGGGTACCTATT----------------------- Brachionus_angularis_1 ATAGACGCAGGCT-----------------AAAAATCATGT--ATGCTCGTATAGCATT-CATGTCGGGTACCTATTTA--------------------- Brachionus_angularis_2 ATAGACGCAGGCT-----------------AAAAATCATGT--ATGCTCGTATAGCATT-CATGTCGGGTACCTATT----------------------- Brachionus_angularis_3 ATAGACGCAGGCT-----------------AAAAATCATGT--ATGCTCGTATAGCATT-CATGTCGGGTACCTATT----------------------- Plationus_patulus ATAGTCAT----------------------AAAATCCATAT--TTGCGTG---AATATG----GTCGGGTACCTATGTATGTGATTTTCTATGAAATTCA Brachionus_dimidiatus_3 AT-------TGCTCAA-------TTCAAATAAAATCCACTC--ATACGTT---TGCGTG----GTCGGGTACCTTTAATTGT-ATTTTTAAAAGAATGCA Brachionus_dimidiatus_1 AT-------TGCTCAA-------TTCAAATAAAATCCACTC--ATACGTT---TGCGTG----GTCGGGTACCTTTAATTGT-ATTTTTAAAAGAATGCA Brachionus_dimidiatus_2 AT-------TCCTCAA-------TTTGAATAAAATCCACTC--ATACGTG---TGCGTG----GTCGGGTACCTTTAATT---GTATTTTTAACAAATAC Brachionus_manjavacas_1 AT-------TTCTCAT----------TCAAAAAATCCACTC--ATACATT---TGTGTG----GTCGGGTACCTTTAATTGT----ATTCTAATGAATAC Brachionus_manjavacas_2 AT-------TTCTCAT----------TCAAAAAATCCACTC--ATACATT---TGTGTG----GTCGGGTACCTTTAATTGT-ATTCTAATG---AATAC Brachionus_sp._Austria_1 AT-------TTCTCAT----------TCAAAAAATCCACTC--ATACGTT---TGTGTG----GTCGGGTACCTTTAATTGA----ATTCTAATGAATTC Brachionus_sp._Austria_2 AT-------TTCTCAT----------TCAAAAAATCCACTC--ATACGTT---TGCGTG----GTCGGGTACCTTTAATTGA----ATTCTAATCAATTC Brachionus_sp._Austria_3 AT-------TTCTCAT----------TCAAAAAATCCACTC--ATACGTT---TGCGTG----GTCGGGTACCTTTAATTGA----ATTCTAATCAATTC Brachionus_sp._Nevada_1 AT-------TTCTCAT----------TCAAAAAATCCACTC--ATACGTT---TGTGTG----GTCGGGTACCTTTAATTGT----TTTCTAATGAATAC Brachionus_plicatilis_1 AT-------TTCTCAT----------CCAAAAAATCCACTC--ATACGTT---TGTGTG----GTCGGGTACCTTTAATTGT-ATTCAAATGA--ATGCA Brachionus_plicatilis_2 AT-------TTCTCAT----------CCAAAAAATCCACTC--ATACGTT---TGTGTG----GTCGGGTACCTTTAATTGT----ATTCTAATGAATGC Brachionus_plicatilis_3 AT-------TTCTCAT----------CCAAAAAATCCACTC--ATACGTT---TGTGTG----GTCGGGTACCTTTAATTGT-ATTCTAATGA--ATGCA Brachionus_plicatilis_4 AT-------TTCTCAT----------CCGAAAAATCCACTC--ATACGTT---TGTGTG----GTCGGGTACCTTTAATTGT----ATTCTAATGAATGC Brachionus_rotundiformis_1 AT-------TGCTCAA----------TCATAAAATCCACAC--AAACGTT---TGTGTG----GTCGGGTACCTTTAATTGT-ATTCTAGTGG--ATACA Brachionus_rotundiformis_2 AT-------TGCTCAA----------TCATAAAATCCACAC--AAACGTT---TGTGTG----GTCGGGTACCTTTAATTGT----ATTCTAGTCGATAC Brachionus_sp._Tiscar_1 AT-------TGTTCAA-----------TCAAAAATCCACAC--ATACTATTTGTGTGTG----GTCGGGTACCTTTAATTAA-ATTCATTTGG--ATTTA Brachionus_sp._Tiscar_2 AT-------TGTTCAA-----------TCAAAAATCCACAC--ATACTATTTGTGTGTG----GTCGGGTACCTTTAATTAA-ATTCATTTGG--ATTTA Brachionus_sp._Cayman_1 AT-------TGTTCAA-----------TCAAAAATCCACAC--ATACTTTTTGTGTGTG----GTCGGGTACCTTTAATTAA-ATTCATTTGA--ATTTA Brachionus_sp._Cayman_2 AT-------TGTTCAA-----------TCAAAAATCCACAC--ATACTTTTTGTGTGTG----GTCGGGTACCTTTAATTAA-ATTCATTTGA--ATTTA Brachionus_ibericus_1 AT-------TGCTCAA-----------TCAAAAATCCACAC--ATGCTTT--GTGTGTG----GTCGGGTACCTTTAATTAAATTCATTTG----AATTT Brachionus_ibericus_2 AT-------TGCTCAA-----------TCAAAAATCCACAC--ATGCTTT--GTGTGTG----GTCGGGTACCTTTAATTAA-ATTCATTTGA--ATTTA Brachionus_ibericus_3 AT-------TGCTCAA-----------TCAAAAATCCACAC--ATGCTTT--GTGTGTG----GTCGGGTACCTTTAATTAA-ATTCATTTGA--ATTTA Brachionus_ibericus_4 AT-------TGCTCAA-----------TCAAAAATCCACAC--ATGCTTT--GTGTGTG----GTCGGGTACCTTTAATTAA-ATTCATTTG---AATTT Brachionus_sp._Almenara_1 AT-------TGCTCAA-----------TCAAAAATCCACAC--ATTCTTT--GTGCCTG----GTCGGGTACCTTTAATTAA-ATTCATTTGA--ATTTA Brachionus_sp._Almenara_2 AT-------TGCTCAA-----------TCAAAAATCCACAC--ATTCTTT--GTGCCTG----GTCGGGTACCTTTAATTAA-ATTCATTTG---AATTT Brachionus_calyciflorus_1 AA-------AGCTCGG--------CGTATTCAAATCCATGC--ATGCTCT---TGTATG----GTCGGGTACTATT------------------------ Brachionus_calyciflorus_2 AA-------AGCTCGG-------CGTATTCAAATTCCATGC--ATGCTCT---TGTATG----GTCGGGTACCTATT----------------------- Brachionus_calyciflorus_3 AA-------AACTCGG-------CGTATTCAAATTCCATGC--ATGCTCT---TGTATG----GTCGGGTACCTAAT----------------------- Brachionus_calyciflorus_4 AA-------AATTCGG--------CGTATAAAAATCCATGC--ATGCTCT---TGTATG---AGTCGGGTACCTTAT----------------------- Brachionus_calyciflorus_5 AG-------AACTTGG-------CGTATTTAAATTCCATAC--ATGCTCT---TGTATG----GTCGGGTACCTAAT----------------------- Brachionus_sessilis_Doirani_1 AT-------GACTAGC----------CATAGAAATCCATAC--ATGCTTATCTTGTATG----GTCGGGTACCTAAGCT----ATGCTTGTAACATAGAA Brachionus_sessilis_Doirani_2 AT-------GACTAGC----------CATAGAAATCCATAC--ATGCTTATCTTGTATG----GTCGGGTACCTAAGCT----ATGCTTGTAACATAGAA Brachionus_sessilis_Doirani_3 AT-------GACTAGC----------CATAGAAATCCATAC--ATGCTTATCTTGTATG----GTCGGGTACCTAAGCT----ATGCTTGTAACATAGAA Brachionus_sessilis_Doirani_4 AT-------GACTAGC----------CATAGAAATCCATAC--ATGCTTATCTTGTATG----GTCGGGTACCTAAGCT----ATGCTTGTAACATAGAA Brachionus_sessilis_Doirani_5 AT-------GACTAGC----------CATAGAAATCCATAC--ATGCTTATCTTGTATG----GTCGGGTACCTAAGCT----ATGCTTGTAACATAGCA Brachionus_sessilis_Balaton_1 AT-------GACTAGC----------CATAGAAATCCATAC--ATGCTTATCTTGTATG----GTCGGGTACCTAAGCT----ATGCTTGTAACATAGCA Brachionus_sessilis_Balaton_2 AT-------GACTAGC----------CATAGAAATCCATAC--ATGCTTATCTTGTATG----GTCGGGTACCTAAGCT----ATGCTTGTAACATAGCA Brachionus_rubens_1 AT-------GACTAGCAAGTTAGTTAAATTAAA-TCCATGC--ATGCTTATCTTGTATG----GTCGGGTACC--TAAGTAT-GTTCAATTTATGTAGCA Brachionus_rubens_2 AT-------GACTAGCAAGTTAGTTAAATTAAA-TCCATGC--ATGCTTATCTTGTATG----GTCGGGTACCTAAGTAT---GTTCAATTTATGTAGCA Brachionus_rubens_3 AT-------GACTAGC---------ACAAACAAATCCATAC--ATGCTTATCTTGTATG----GTCGGGTACCTAAGTATGC--------TTACATAAGC Brachionus_urceolaris ---------AGCTTGC------------TTTAAATCCATAC--ATGCGTATCTTGTATG----GTCGGGTACCTATGAA--------TGTGTATTTAACA Brachionus_leydigii AT-------GGCTTGC-----------ATTAAAATCCATAC--ATGCTTATCTTGTATG----GTCGGGTACCTAAGTATGTGTCTTG-------TAACA Brachionus_quadridentatus_1 AT-------GGCTTGC-----------ATTAAAATCCATAC--ATGCTTATCTTGTATG----GTCGGGTACCTAAGTATGT-GTCCT-------GAACA Brachionus_quadridentatus_2 AT-------GGCTTGC-----------ATTAAAATCCATAC--ATGCTTATCTTGTATG----GTCGGGTACCTAAGTATGT-GTCCT-------GAACA Lecane_bulla TTTCTTAAGC------AGCATT--GATTAGTTGTTGC-AAGGTTTAAAGACTATTAATCTTA-----ATTAATAGCGCCTGTGTGCAAATTGATTTTTCT Brachionus_bidentatus ----TTAAGCGATTCTCGCAATC-----TATGATCGTGTTGGTTTGAAGATAGTTATTTCTC----TAATAACTACGCCCGC-------TTAGCATTTAA Brachionus_forficula TTTTTTAAGCGATCCGAGCCT---AATTATGGATCGTGTTGGTTTGAAGATAGTTCATTCTCATACAGTGAACTACGCCCGC-------TCACTATAGCC Brachionus_diversicornis TTTTGTAAGCGATCCGAGCCTAA----TTATGGTCGTGTTGGTTTGAAGATAGTTCATTCTCATACAGTGAACTACGCCCGC-------TCACTATAGCC Brachionus_angularis_1 ------AAGCGATCCGAGCTA---AAAACAGGATCGTGTTGGTTTGAAGATAGTTCATTCTCATATAGTGAACTACGCCCGC-------ATAATT----A Brachionus_angularis_2 ----TAAAGCGATCCGAGCTAAA---AACAGGATCGTGTTGGTTTGAAGATAGTTCATTCTCATATAGTGAACTACGCCCGC-------ATAATT----A Brachionus_angularis_3 ----CAAAGCGATCCGAGCTAAA---AACAGGATCGTGTTGGTTTGAAGATAGTTCATTCTCATATAGTGAACTACGCCCGC-------ATAATT----A Plationus_patulus CATCATAAGCGGTAA-TGCTTTT---------GCCGT-ATGGTTTCAAGATAATTTAACAAA-----TTAAATTACGCCCGC-------TTAGCTAAAAC Brachionus_dimidiatus_3 ATT-GTAAGCGATTA-AGCTTTT-----CATGATCGTGAAGGTTTGAAGATAGTTCATCTCA----ACTGAACTACGCCCGC-------TTAGCCTA-AA Brachionus_dimidiatus_1 ATT-GTAAGCGATTA-AGCTTTT-----CATGATCGTGAAGGTTTGAAGATAGTTCATCTCA----ACTGAACTACGCCCGC-------TTAGCCTA-AA Brachionus_dimidiatus_2 AATTGTAAGCGATCA-AGCTTTT----TGACGATCGTGATGGTTTGAAGATAGTTCATCTAA----AGTGAACTACGCCCGC-------TCGGCATT--A Brachionus_manjavacas_1 AATTGTAAGCGATCA-TGCTTTA------TTGATTGTGACGGTTTGAAGATAGCTCATTCTA----AATGAACTACGCCCGC-------TTAGCTTT--A Brachionus_manjavacas_2 AATTGTAAGCGATCA-TGCTTTA------TTGATTGTGACGGTTTGAAGATAGCTCATTCTA----AATGAACTACGCCCGC-------TTAGCTTT--A Brachionus_sp._Austria_1 AATTGTAAGCGATCA-GGCTTTA------ATGATCGTGACGGTTTGAAGATAGCTCATTTGA----AATGAACTACGCCCGT-------TTAGCATC--A Brachionus_sp._Austria_2 AATTGTAAGCGATCA-GGCTTTA------ATGATCGTGACGGTTTGAAGATAGCTCATTTGA----AATGAACTACGCCCGT-------TTAGCCTC--A Brachionus_sp._Austria_3 AATTGTAAGCGATCA-GGCTTTA------ATGATCGTGACGGTTTGAAGATAGCTCATTTGA----AATGAACTACGCCCGT-------TTAGCATC--A Brachionus_sp._Nevada_1 AATTGTAAGCGATCA-AGCTTTA------ATGATCGTGACGGTTTGAAGATAGCTCATTTTA----AATGAACTACGCCCGT-------TAAGCATTTAG Brachionus_plicatilis_1 ATT-GTAAGCGATCT-AGCTTTA------ATGATCGTGACGGTTTGAAGATAGCTCATTTGA----AATGAACTACGCCCGT-------GAAGCATTTAG Brachionus_plicatilis_2 AATTGTAAGCGATCT-AGCTTTA------ATGATCGTGATGGTTTGAAGATAGCTCATTTCA----AATGAACTACGCCCGT-------GAAGCATTTAG Brachionus_plicatilis_3 ATT-GTAAGCGATCT-AGCTTTA------ATGATCGTGATGGTTTGAAGATAGCTCATTTCA----AATGAACTACGCCCGT-------GAAGCATTTAG Brachionus_plicatilis_4 AATTGTAAGCGATCT-AGCTTTA------ATGATCGTGATGGTTTGAAGATAGCTCATTTCA----AATGAACTACGCCCGT-------GAAGCATTTAG Brachionus_rotundiformis_1 ATT-ATAAGCGATCA-AGCATTT------GTGATCGTGACGGTTTGAAGATAGTTCATCGTA----AATGAACTACGCCCGC-------TTAGCTTT-AA Brachionus_rotundiformis_2 AATTATAAGCGATCA-AGCATTT------GTGATCGTGACGGTTTGAAGATAGTTCATCGTA----AATGAACTACGCCCGC-------TTAGCTTT-AA Brachionus_sp._Tiscar_1 ATT-GTAAGCGATCA-AGCTTTA----TATCGATCGTGATGGTTTGAAGATAGCTCATCATA----TATGAACTACGCCCGT-------TTAGCTTATAA Brachionus_sp._Tiscar_2 ATT-GTAAGCGATCA-AGCTTTA----TATCGATCGTGATGGTTTGAAGATAGCTCATCATA----TATGAACTACGCCCGT-------TTAGCTTATAA Brachionus_sp._Cayman_1 ATT-GTAAGCGATCA-AGCTTTA----TATGGATCGTGATGGTTTGAAGATAGCTCATCATA----TGTGAACTACGCCCGT-------TTAGCTTATAA Brachionus_sp._Cayman_2 ATTCGTAAGCGATCA-AGCTTTA----TATGGATCGTGATGGTTTGAAGATAGCTCATCATA----TGTGAACTACGCCCGT-------TTAGCTTATAA Brachionus_ibericus_1 AATTGTAAGCGATCA-AGCATTTTTATTATGGATCGTGATGGTTTGAAGATAGTTCATCATA----TGTGAACTACGCCCGT-------TTAGCTTTTAA Brachionus_ibericus_2 ATT-GTAAGCGATCA-AGCATTTTTATTATGGATCGTGATGGTTTGAAGATAGTTCATCATA----TGTGAACTACGCCCGT-------TTAGCTTTTAA Brachionus_ibericus_3 ATT-GTAAGCGATCA-AGCATTTTTATTATGGATCGTGATGGTTTGAAGATAGTTCATCATA----TGTGAACTACGCCCGT-------TTAGCTTTTAA Brachionus_ibericus_4 AATTGTAAGCGATCA-AGCATTTTTATTATGGATCGTGATGGTTTGAAGATAGTTCATCATA----TGTGAACTACGCCCGT-------TTAGCTTTTAA Brachionus_sp._Almenara_1 ATT-GTAAGCGATCA-AGCTTTCTTATTTTTGATCGTGATGGTTTGAAGATAGTTCATCACA----TATGAACTACGCCCGT-------TTAGCTTTTAA Brachionus_sp._Almenara_2 AATTGTAAGCGATCA-AGCTTTCTTATTTTTGATCGTGATGGTTTGAAGATAGTTCATCACA----TATGAACTACGCCCGT-------TTAGCTTTTAA Brachionus_calyciflorus_1 ----ATAAGCGATCT-AGCAAAT-------TGATCGTGTTGGTTTGAAGATAGTTCATCCCA------TGAACTACGCCCGT--------------TCAA Brachionus_calyciflorus_2 ----TTAAGCGATCT-TGTGCTA-----ATTGATCGTGTTGGTTTGAAGATAGTTCATCCTA----TGTGAACTACGCCCGC-------TCAA-----AT Brachionus_calyciflorus_3 ----TTAAACGGTCT-AGCTTTT--------GATCGTGTTGGTTTGAAGATAGTTCATCCAA----TGTGAACTACGCCCGC-------TAAATT----- Brachionus_calyciflorus_4 ----TTAAGCGATCT-TGCTTTT---------ATCGTGTTGGTTTGAAGATAGTTCATCCCA----TGTGAACTACGCCCGC-------TGAATT----- Brachionus_calyciflorus_5 ----TTAAGCGGTCT-TGCTTCT--------GATCGTGTTGGTTTGAAGATAGTTCATCCCA----TGTGAACTACGCCCGC-------TAAATT----- Brachionus_sessilis_Doirani_1 TAGCATAAGCGATCA-AGCTCTA---ATTTAGATCGT-ATGGTTTGAAGATAGTTCATCCTA----TGTGAACTACGCCCGC-------CAAAGCATTAA Brachionus_sessilis_Doirani_2 TAGCATAAGCGATCA-AGCTCTA---ATTTAGATCGT-ATGGTTTGAAGATAGTTCATCCTA----TGTGAACTACGCCCGC-------CAAAGCATTAA Brachionus_sessilis_Doirani_3 TAGCATAAGCGATCA-AGCTCTA---ATTTAGATCGT-ATGGTTTGAAGATAGTTCATCCTA----TGTGAACTACGCCCGC-------CAAAGCATTAA Brachionus_sessilis_Doirani_4 TAGCATAAGCGATCA-AGCTCTA---ATTTAGATCGT-ATGGTTTGAAGATAGTTCATCCTA----TGTGAACTACGCCCGC-------CAAAGCATTAA Brachionus_sessilis_Doirani_5 TAGCATAAGCGATCA-AGCTCTA---ATTTAGATCGT-ATGGTTTGAAGATAGTTCATCCTA----TGTGAACTACGCCCGC-------CAAAGCATTAA Brachionus_sessilis_Balaton_1 TAGCATAAGCGATCA-AGCTCTA---ATTTAGATCGT-ATGGTTTGAAGATAGTTCATCCTA----TGTGAACTACGCCCGC-------CAAAGCATTAA Brachionus_sessilis_Balaton_2 TAGCATAAGCGATCA-AGCTCTA---ATTTAGATCGT-ATGGTTTGAAGATAGTTCATCCTA----TGTGAACTACGCCCGC-------CAAAGCATTAA Brachionus_rubens_1 TAC-ATAAGCGATCA-AGCTTAA------GTGATCGT-ATGGTTTGAAGATAGTTCATCTTA----TGTGAACTACGCCCGC--------AAAGCATTAA Brachionus_rubens_2 TAC-ATAAGCGATCA-AGCTTAA------GTGATCGT-ATGGTTTGAAGATAGTTCATCTTA----TGTGAACTACGCCCGC--------AAAGCATTAA Brachionus_rubens_3 ATACATAAGCGATCA-AGCCATT----TATGGATCGT-TTGGTTTGAAGATAGTTCATCTTA----AATGAACTACGCCCGC-------AAAGCATT--- Brachionus_urceolaris CATCGTAAGCGATCA-TGC-----TAATCAGGATCGT-TTGGTTTGAAGATAGTTCATCTTA----AATGAACTACGCCCGC-------TTAGCTAACTA Brachionus_leydigii CATCATAAGCGATCA-AGCAAAC-------CGATCGT-TTGGTTTGAAGATAGTTCATCATA----AATGAACTACGCCCGC-------TAAAAGCTTAT Brachionus_quadridentatus_1 CATCATAAGCGATCA-AGCAACC-------CGATCGT-TTGGTTTGAAGATAGTTCATCTTA----AATGAACTACGCCCGC-----TAATAGCTTTTTT Brachionus_quadridentatus_2 CATCATAAGCGATCA-AGCAACC-------CGATCGT-TTGGTTTGAAGATAGTTCATCTTA----AATGAACTACGCCCGC-----TAATAGCTTTTTT Lecane_bulla TAAAATG--------ACATTTTTTA-------ATTACTATCTTTTAAAGAATTATTAAGTCTTTGATT-----------TAAAAATTC---TTAAATTTA Brachionus_bidentatus A-------TTCTATCACATTTTCCATTTAAACCATTGTTTTTGT------TGTGTTTGTTGTTTGGTT----GAGCTTTTAAGCACTT-CATAGTGTTTA Brachionus_forficula AAACTAAACT-----ATATTT------------ATTTTATTTAC-----CATTGTTGTATGTGTTGTATTCGTAAGCTGTAAATACAC-----ACGTTTA Brachionus_diversicornis AAACTAAACT-----ATATTT------------ATTTTATTTAC-----CATTGTTGTATGTGTTGTATTCGTAAGCTGTAAATACAC-----ACGTTTA Brachionus_angularis_1 GCAAAACATTAAACTACATTT------------ATTTTATTTAC-----CATTGTTGTATGTGTTGTATTAGTAAGATGTAAAAACGC---GTGCACTTG Brachionus_angularis_2 GCAAAACATTAAACTACATTT------------ATTTTATTTAC-----CATTGTTGTATGTGTTGTATTAGTAAGATGTAAAAACGC---GTGCACTTG Brachionus_angularis_3 GCAAAACATTAAACTACATTT------------ATTTTATTTAC-----CATTGTTGTATGTGTTGTATTAGTAAGATGTAAAAACGC---GTGCACTTG Plationus_patulus ATAACTACATTT---ACATTTTATA---------TTTTATTTTA------GTTGTTTTATTGTGAAAA----AAAGTCTTTAATATTC-TATAATATTTA Brachionus_dimidiatus_3 AAAAATATTT-----ACATTATTAACATAAA---TTTTGTTAAA----ACATTGTTTTACTAA----------AACGAACACTAACAC---AAGTGTTCA Brachionus_dimidiatus_1 AAAAATATTT-----ACATTATTAACATAAA---TTTTGTTAAA----ACATTGTTTTACTAA----------AACGAACACTAACAC---AAGTGTTCA Brachionus_dimidiatus_2 ATAAAAAACT-----ACATTATTTTCATAAA---TTTTGTTTCA----AAATTGTTTTAAATAA---------AACGAACACTTGCAA---AAGTGTCCT Brachionus_manjavacas_1 ATAAATATCT-----ACATTTTATTTATAAA---CTTTGTTTTT----ATGATGTTTTGCTT--------------AAATGAACGCTTATTAAGTTGTTC Brachionus_manjavacas_2 ATAAATATCT-----ACATTTTATTTATAAA---CTTTGTTTTT----ATGATGTTTTGCTT------------AAATGAACGCTTAT-TAAGTTGTTCT Brachionus_sp._Austria_1 AGAAATATCT-----ACATTTTACATATAAA---CTTTGTTATT----ATGATGTTTTACTTA----------AATGAACGCTTGTTT---AAGAGTTCT Brachionus_sp._Austria_2 AGAAATATCT-----ACATTTTACATATAAA---CTTTGTTATT----ATGATGTTTTACTTA----------AATGAACGCTTGTTT---AAGAGTTCT Brachionus_sp._Austria_3 AGAAATATCT-----ACATTTTACATATAAA---CTTTGTTATT----ATGATGTTTTACTTA----------AATGAACGCTTGTTT---AAGAGTTCT Brachionus_sp._Nevada_1 AAATATCT-------ACATTTTACATATAAA---CTTTGTTTTT----ATGATGTTTTACTT--------------AAATGAACGCTTATTAAGTGTTCT Brachionus_plicatilis_1 A--AATATCT-----ACATTTTACATATAAA---CTTTGTTTTT----ATGATGTTTT-ACTTAAATG-----AACGCCTA-----TT---AAGTGTTCT Brachionus_plicatilis_2 AAATATCT-------ACATTTTACATATAAA---CTTTGTTTTT----ATGATGTTTTACTT--------------AAATGAACGCTTATTAAGTGTTCT Brachionus_plicatilis_3 A--AATATCT-----ACATTTTACATATAAA---CTTTGTTTTT----ATGATGTTTT-ACTTAAATG-----AACGCTTA-----TT---AAGTGTTCT Brachionus_plicatilis_4 AAATATCT-------ACATTTTACATATAAA---CTTTGTTTTT----ATGATGTTTTACTT--------------AAATGAACGCTTATTAAGTGTTCT Brachionus_rotundiformis_1 ATAAATGATC-----ACATTTTATA--TATAAACTTTTGTTTGT----ATGATGTTTT-ACTAAAATG-----AACACTTAAATTTAT---AAGTGCTCT Brachionus_rotundiformis_2 ATAAATGATC-----ACATTTTATA--TATAAACTTTTGTTTGT----ATGATGTTTTACTAA----------AACGAACACTTATAT---AAGTGCTCT Brachionus_sp._Tiscar_1 ATAAATATAT-----ACATTGTAAA-TTATAAAATTTTGTTTTT----CTAATGTTTT-ACTAAAATG-----AACGCTTA-TTATTT---AAGTGTTCT Brachionus_sp._Tiscar_2 ATAAATATAT-----ACATTGTAAA-TTATAAAATTTTGTTTTT----CTAATGTTTT-ACTAAAATG-----AACGCTTA-TTATTT---AAGTGTTCT Brachionus_sp._Cayman_1 ATAAATATAT-----ACATTGT-TAATTATAAAATTTTGTTTTTTTTGTTAATGTTTTA-CTAAAATG-----AGCGCTTATTATTAT---AAGTGTTCT Brachionus_sp._Cayman_2 ATAAATATAT-----ACATTGT-TAATTATAAAATTTTGTTTTATTTGTTAATGTTTTA-CTAAAATG-----AGCGCTTATTTTTAT---AAGTGTTCT Brachionus_ibericus_1 ATAAATATTT-----ACATTTTATACATATAAAATTTTGTTTTT----ATCATGTTTTACTAA----------AATGAACGCTTATTTCATAAGTGTTCT Brachionus_ibericus_2 ATAAATATTT-----ACATTTTATACATATAAAATTTTGTTTTT----ATCATGTTTT-ACTAAAATG-----AACGCTTA-TTTCAT---AAGTGTTCT Brachionus_ibericus_3 ATAAATATTT-----ACATTTTATACATATAAAATTTTGTTTTT----ATCATGTTTT-ACTAAAATG-----AACGCTTA-TTTCAT---AAGTGTTCT Brachionus_ibericus_4 ATAAATATTT-----ACATTTTATACATATAAAATTTTGTTTTT----ATCATGTTTTA-CTAAAATG-----AACGCTTA---TTTC-ATAAGTGTTCT Brachionus_sp._Almenara_1 ATAAATATTT-----ACATTTTATATTTATAAAATTTTGTTTAT----ATGATGTTTT-ACTAAAATG-----AATGCTTAATAA--T---AAGTGTTCT Brachionus_sp._Almenara_2 ATAAATATTT-----ACATTTTATATTTATAAAATTTTGTTTAT----ATGATGTTTTACTAA----------AATGAATGCTTATTA-ATAAGTGTTCT Brachionus_calyciflorus_1 ATGCATAAAATTATAACATTTTATA----AAAATTTCTATTCTT------AGTGTTGTATTCTTAATT-----AAAAAATAAGTGCTT---CGGCGCTTA Brachionus_calyciflorus_2 GCATTAAACTTTATAACATTTTATA----AAAATTTCTATTCTT------AGTGTTGTATACTTAATT-----AAAAAATAAGTGCTT---CGGTGCTTA Brachionus_calyciflorus_3 GCATAAAATTTTAAAACATTTTATA----AAAACTTCTATTCTT------AGTGTTGTATTTTTAATT-----AAAAAATGAGTTCTT---CGGGACTTA Brachionus_calyciflorus_4 GCATAAAATTTTATAACATTTTATA----AAAACTTCTATTCTT------AGTGTTGTTTTTTTAATT-----AAAAAATAAGTGCTT---CGGTACTTA Brachionus_calyciflorus_5 GCATAAAATTTTAAAACATTTTATA----AAAACTCCTATTCTT------AGTGTTGTATTTTTAATT-----AAAAAATAAGTGCTT---CGGTGCTTA Brachionus_sessilis_Doirani_1 AT---TATTTTAATTACATTTTATA--TAAATGATTTTATTGTT------AGTGTTGTATTC------------ATGTATAAACGCTT-----GTGCTGA Brachionus_sessilis_Doirani_2 AT---TATTTTAATTACATTTTATA--TAAATGATTTTATTGTT------AGTGTTGTATTC------------ATGTATAAACGCTT-----GTGCTGA Brachionus_sessilis_Doirani_3 AT---TATTTTAATTACATTTTATA--TAAATGATTTTATTGTT------AGTGTTGTATTC------------ATGTATAAACGCTT-----GTGCTGA Brachionus_sessilis_Doirani_4 AT---TATTTTAATTACATTTTATA--TAAATGATTTTATTGTT------AGTGTTGTATTC------------ATGTATAAACGCTT-----GTGCTGA Brachionus_sessilis_Doirani_5 AT---TATTTTAATTACATTTTATA--TAAATGATTTTATTGTT------AGTGTTGTATTC------------ATGTATAAACGCTT-----GTGCTGA Brachionus_sessilis_Balaton_1 AT---TATTTTAATTACATTTTATA--TAAATGATTTTATTGTT------AGTGTTGTATTC------------ATGTATAAACGCTT-----GTGCTGA Brachionus_sessilis_Balaton_2 AT---TATTTTAATTACATTTTATA--TAAATGATTTTATTGTT------AGTGTTGTATTC------------ATGTATAAACGCTT-----GTGCTGA Brachionus_rubens_1 ATTAGCATTTAAATTACATTTTATA--AAAATGATTGTGATTGT-----TAGTGTTGTATTC------------ATGTATAAACGCTT---AA------- Brachionus_rubens_2 ATTAGCATTTAAATTACATTTTATA--AAAATGATTGTGATTGT-----TAGTGTTGTATTC------------ATGTATAAACGCTT------------ Brachionus_rubens_3 --AAAAATCTTAACTACATTTTATA--AAAATGATTTTGTTGTT------AGTGTTGTATTC------------ATGTATAAACGCGC-------GTTTA Brachionus_urceolaris ATATATTAT------ACATTTTATA--AAAATGTTTTTATT-------ATAGTGTTGTATTC------------ATGTGTAAACGCTT---TGAATTTTT Brachionus_leydigii TTAAATCTA------ACATTTTATA-----AAAATGTTTTTTGT------AGTGTTGTATTT------------ATGTAAAAATACGC---TATGGTTTT Brachionus_quadridentatus_1 AAATCTA--------ACATTTTATA--AAAATGTTTTTG----------TAGTGTTGTATTT------------ATGTAAAAATGCGC---TATGATTTA Brachionus_quadridentatus_2 AAATCTA--------ACATTTTATA--AAAATGTTTTTGT----------AGTGTTGTATTT------------ATGTAAAAATGCGC---TATGATTTA Lecane_bulla TT------------AACAACCCTATGCG Brachionus_bidentatus TT--------------AGACTAACA--- Brachionus_forficula TGTGTGTGTTTGTAAACAACTT------ Brachionus_diversicornis TGTGTGTGTTTGTAAACAACTT------ Brachionus_angularis_1 TGCTCGTGTTTGTCAACAACTT------ Brachionus_angularis_2 TGCTCTTGTTTGTCAACAACTTAAA--- Brachionus_angularis_3 TGCTCTTGTTTGTCAACAACTTAAA--- Plationus_patulus -----------------------GACAT Brachionus_dimidiatus_3 TT--------------TAACTAAAACAC Brachionus_dimidiatus_1 TT--------------TAACTAAAACAC Brachionus_dimidiatus_2 TT--------------TAACTAAAACAC Brachionus_manjavacas_1 TT-----------TTAAAACTAAAACAC Brachionus_manjavacas_2 TT------------TAAAACTAAAACAC Brachionus_sp._Austria_1 TT------------TAAAACTAAAACAC Brachionus_sp._Austria_2 TT------------TAAAACTAAAACAC Brachionus_sp._Austria_3 TT------------TAAAACTAAAACAC Brachionus_sp._Nevada_1 TT------------TAAAACTAAAACAC Brachionus_plicatilis_1 TT------------TAAAACTAAAACAC Brachionus_plicatilis_2 TT------------TAAAACTAAAACAC Brachionus_plicatilis_3 TT------------TAAAACTAAAACAC Brachionus_plicatilis_4 TT------------TAAAACTAAAACAC Brachionus_rotundiformis_1 TT--------------TAACTAAAACAC Brachionus_rotundiformis_2 TT--------------TAACTAAAACAC Brachionus_sp._Tiscar_1 TT--------------TAACTAAAACAC Brachionus_sp._Tiscar_2 TT--------------TAACTAAAACAC Brachionus_sp._Cayman_1 TT--------------TAACTAAAACAC Brachionus_sp._Cayman_2 TT--------------TAACTAAAACAC Brachionus_ibericus_1 TT--------------TAACTAAAACAC Brachionus_ibericus_2 TT--------------TAACTAAAACAC Brachionus_ibericus_3 TT--------------TAACTAAAACAC Brachionus_ibericus_4 TT--------------TAACTAAAACAC Brachionus_sp._Almenara_1 TT--------------TAACTAAAACAC Brachionus_sp._Almenara_2 TT--------------TAACTAAAACAC Brachionus_calyciflorus_1 TA-----------GTTTAACTTAAATAC Brachionus_calyciflorus_2 TA-----------CTTTAACTTAAATAC Brachionus_calyciflorus_3 TG-----------ATTTAACTTTAATAC Brachionus_calyciflorus_4 TG-----------ATTTAACT------- Brachionus_calyciflorus_5 TG-----------ATTTAACTTTAATAC Brachionus_sessilis_Doirani_1 TT--GTCCAGTGCAATTAGCTAGAGCGA Brachionus_sessilis_Doirani_2 TT--GTCCAGTGCAATTAGCTAGAGCGA Brachionus_sessilis_Doirani_3 TT--GTCCAGTGCAATTAGCTAGAGCGA Brachionus_sessilis_Doirani_4 TT--GTCCAGTGCAATTAGCTAGAGCGA Brachionus_sessilis_Doirani_5 TT--GTCCAGTGCAATTAGCTAGAGCGA Brachionus_sessilis_Balaton_1 TT--GTCCAGTGCAATTAGCTAGAGCGA Brachionus_sessilis_Balaton_2 TT--GTCCAGTGCAATTAGCTAGAGCGA Brachionus_rubens_1 --------------AGCAGCGAAAGCAG Brachionus_rubens_2 ------------AAAGCAGCGAAAGCAG Brachionus_rubens_3 TT--GACTTGTGCAATTAGCGATAGCGA Brachionus_urceolaris CA--------------TAGCGA------ Brachionus_leydigii TT---------------GATCATTGCGT Brachionus_quadridentatus_1 TT--------------TAATCATTTCGT Brachionus_quadridentatus_2 TT--------------TAATCATTTCGT ; END; BEGIN TREES; Title Bayesian_tree_of_ITS1; LINK Taxa = Taxa_ITS1; TRANSLATE 1 Lecane_bulla, 2 Brachionus_bidentatus, 3 Brachionus_forficula, 4 Brachionus_diversicornis, 5 Brachionus_angularis_1, 6 Brachionus_angularis_2, 7 Brachionus_angularis_3, 8 Plationus_patulus, 9 Brachionus_dimidiatus_3, 10 Brachionus_dimidiatus_1, 11 Brachionus_dimidiatus_2, 12 Brachionus_manjavacas_1, 13 Brachionus_manjavacas_2, 14 Brachionus_sp._Austria_1, 15 Brachionus_sp._Austria_2, 16 Brachionus_sp._Austria_3, 17 Brachionus_sp._Nevada_1, 18 Brachionus_plicatilis_1, 19 Brachionus_plicatilis_2, 20 Brachionus_plicatilis_3, 21 Brachionus_plicatilis_4, 22 Brachionus_rotundiformis_1, 23 Brachionus_rotundiformis_2, 24 Brachionus_sp._Tiscar_1, 25 Brachionus_sp._Tiscar_2, 26 Brachionus_sp._Cayman_1, 27 Brachionus_sp._Cayman_2, 28 Brachionus_ibericus_1, 29 Brachionus_ibericus_2, 30 Brachionus_ibericus_3, 31 Brachionus_ibericus_4, 32 Brachionus_sp._Almenara_1, 33 Brachionus_sp._Almenara_2, 34 Brachionus_calyciflorus_1, 35 Brachionus_calyciflorus_2, 36 Brachionus_calyciflorus_3, 37 Brachionus_calyciflorus_4, 38 Brachionus_calyciflorus_5, 39 Brachionus_sessilis_Doirani_1, 40 Brachionus_sessilis_Doirani_2, 41 Brachionus_sessilis_Doirani_3, 42 Brachionus_sessilis_Doirani_4, 43 Brachionus_sessilis_Doirani_5, 44 Brachionus_sessilis_Balaton_1, 45 Brachionus_sessilis_Balaton_2, 46 Brachionus_rubens_1, 47 Brachionus_rubens_2, 48 Brachionus_rubens_3, 49 Brachionus_urceolaris, 50 Brachionus_leydigii, 51 Brachionus_quadridentatus_1, 52 Brachionus_quadridentatus_2; TREE con_50_majrule = (1:0.1189059,8:0.03287262,((((2:0.07598009,((3:0.001167344,4:0.002887657):0.01520448,(5:0.002863684,(6:5.083192E-4,7:7.400511E-4):0.002665029):0.01939636):0.04319785):0.02770943,(34:0.01565361,(35:0.007385728,((36:0.007606918,38:0.004521439):0.003141219,37:0.00984606):0.007557181):0.006118992):0.02976577):0.01778094,(((9:3.833471E-4,10:3.845262E-4):0.02141053,11:0.01362953):0.01212943,((12:0.003591661,13:0.01374688):0.009508019,((14:4.087232E-4,(15:9.361915E-4,16:3.803394E-4):0.001491319):0.007115475,(17:8.85779E-4,((18:0.003073054,20:5.536183E-4):0.01494483,19:3.831672E-4,21:9.209575E-4):0.004380056):0.005796079):0.003724278):0.01401019,((22:0.0119834,23:0.00221149):0.01022879,((((((24:4.006721E-4,25:4.051446E-4):0.004522136,(26:8.997163E-4,27:9.680587E-4):0.00384962):0.009630105,(29:3.821735E-4,30:3.881981E-4):0.001200575):0.003044837,31:0.001477973):0.003898599,(32:0.003549003,33:0.00389898):0.009953288):0.004679225,28:0.003625611):0.015244):0.006409111):0.04341985):0.02091699,((((((39:3.296745E-4,40:3.44326E-4,41:3.413534E-4,42:3.382005E-4):8.006343E-4,43:3.385532E-4,44:3.402886E-4,45:3.418439E-4):0.01222619,(46:0.002869091,47:4.136123E-4):0.01768605):0.01389657,48:0.009354803):0.01580604,(50:0.01959303,(51:9.172217E-4,52:0.00101264):0.008983302):0.01302786):0.01212506,49:0.02605447):0.007354192):0.03759859); END; BEGIN TREES; Title ML_tree_of_ITS1; LINK Taxa = Taxa_ITS1; TRANSLATE 1 Lecane_bulla, 2 Brachionus_bidentatus, 3 Brachionus_forficula, 4 Brachionus_diversicornis, 5 Brachionus_angularis_1, 6 Brachionus_angularis_2, 7 Brachionus_angularis_3, 8 Plationus_patulus, 9 Brachionus_dimidiatus_3, 10 Brachionus_dimidiatus_1, 11 Brachionus_dimidiatus_2, 12 Brachionus_manjavacas_1, 13 Brachionus_manjavacas_2, 14 Brachionus_sp._Austria_1, 15 Brachionus_sp._Austria_2, 16 Brachionus_sp._Austria_3, 17 Brachionus_sp._Nevada_1, 18 Brachionus_plicatilis_1, 19 Brachionus_plicatilis_2, 20 Brachionus_plicatilis_3, 21 Brachionus_plicatilis_4, 22 Brachionus_rotundiformis_1, 23 Brachionus_rotundiformis_2, 24 Brachionus_sp._Tiscar_1, 25 Brachionus_sp._Tiscar_2, 26 Brachionus_sp._Cayman_1, 27 Brachionus_sp._Cayman_2, 28 Brachionus_ibericus_1, 29 Brachionus_ibericus_2, 30 Brachionus_ibericus_3, 31 Brachionus_ibericus_4, 32 Brachionus_sp._Almenara_1, 33 Brachionus_sp._Almenara_2, 34 Brachionus_calyciflorus_1, 35 Brachionus_calyciflorus_2, 36 Brachionus_calyciflorus_3, 37 Brachionus_calyciflorus_4, 38 Brachionus_calyciflorus_5, 39 Brachionus_sessilis_Doirani_1, 40 Brachionus_sessilis_Doirani_2, 41 Brachionus_sessilis_Doirani_3, 42 Brachionus_sessilis_Doirani_4, 43 Brachionus_sessilis_Doirani_5, 44 Brachionus_sessilis_Balaton_1, 45 Brachionus_sessilis_Balaton_2, 46 Brachionus_rubens_1, 47 Brachionus_rubens_2, 48 Brachionus_rubens_3, 49 Brachionus_urceolaris, 50 Brachionus_leydigii, 51 Brachionus_quadridentatus_1, 52 Brachionus_quadridentatus_2; TREE Imported_tree_0 = (1:0.6415029708710606,(8:0.24385171480448684,((49:0.18523273323757714,((50:0.139988946278387,(51:0.0036531000995696267,52:0.004428500924151832)99:0.058739842379382026):0.08916370348317648,(48:0.06091571380806867,((46:0.017930553398272805,47:1.30045989927037E-6)100:0.1225049559208124,((43:1.30045989927037E-6,(44:1.30045989927037E-6,45:1.30045989927037E-6)33:1.30045989927037E-6)72:1.30045989927037E-6,(40:1.30045989927037E-6,(41:1.30045989927037E-6,(39:1.30045989927037E-6,42:1.30045989927037E-6)16:1.30045989927037E-6)18:1.30045989927037E-6)69:0.003348641719709579)100:0.08525740242765971)97:0.09519803721989409)98:0.1113269739188327)97:0.10046872529063423)75:1.30045989927037E-6,(((34:0.11337995935377684,(35:0.04929517870664485,(37:0.069850841692743,(36:0.05189570407214353,38:0.028241604168757217)58:0.013542958283996787)67:0.048960878157545004)63:0.03121840867223129)92:0.1822302925233633,(2:0.7198803719198392,((3:3.776350015727645E-4,4:0.023121297750925654)99:0.10071743183376371,(5:0.017577554369323258,(6:1.30045989927037E-6,7:0.0038627951234665365)89:0.015614507748899461)93:0.14782747414316158)99:0.35729699067998455)68:0.21196165675843792)51:0.15190734935772918,(((22:0.0853821777543966,23:0.00905520128590696)97:0.07138915631432517,(28:0.020625486553540275,(31:0.0076319646599341045,((29:1.30045989927037E-6,30:1.30045989927037E-6)99:0.006557111083547402,((32:0.005823813128276623,33:0.04169416257143004)94:0.06406370645125452,((24:1.30045989927037E-6,25:1.30045989927037E-6)100:0.026071338765535846,(26:0.0035967753906099072,27:0.003957421637109482)100:0.024900646041038033)100:0.05491392721089039)30:0.013279760022844993)28:0.013507192166308878)47:0.03555803549188949)95:0.10076201896230451)55:0.03547095839769006,((11:0.0942828763482871,(9:1.30045989927037E-6,10:1.30045989927037E-6)100:0.14615524153665221)99:0.07987718978128978,((12:0.022179548369940454,13:0.09075080038875846)98:0.059264830518738196,((14:1.30045989927037E-6,(15:0.003817169589161444,16:1.30045989927037E-6)86:0.007700033579594678)93:0.04977261278686338,(17:0.002737580247113449,((18:0.019877548391044917,20:1.30045989927037E-6)99:0.10207808402255139,(19:1.30045989927037E-6,21:0.0038122061101514442)99:1.30045989927037E-6)84:0.0287429858532021)76:0.03782391094588801)40:0.021485051539484122)99:0.09536154559015254)37:0.012399291949008526)99:0.3348696014848155)67:0.18644629440068722)48:0.3045422465142254)91:0.6415029708710606); END; begin mrbayes; set autoclose = yes; prset applyto = ( all ) ratepr = variable shapepr = fixed ( 1.0300 ) brlensp = unconstrained : Exp ( 100.0 ); lset applyto = ( all ) nucmodel = 4by4 nst = 2 rates = gamma covarion = no; mcmc ngen = 5000000 printfreq = 1000 samplefreq = 1000 nchains = 4 savebrlens = yes; sump; sumt; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 428; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 428; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 428; END; BEGIN TREES; Title MP_trees_of_ITS1; LINK Taxa = Taxa_ITS1; TRANSLATE 1 Lecane_bulla, 2 Brachionus_bidentatus, 3 Brachionus_forficula, 4 Brachionus_diversicornis, 5 Brachionus_angularis_1, 6 Brachionus_angularis_2, 7 Brachionus_angularis_3, 8 Plationus_patulus, 9 Brachionus_dimidiatus_3, 10 Brachionus_dimidiatus_1, 11 Brachionus_dimidiatus_2, 12 Brachionus_manjavacas_1, 13 Brachionus_manjavacas_2, 14 Brachionus_sp._Austria_1, 15 Brachionus_sp._Austria_2, 16 Brachionus_sp._Austria_3, 17 Brachionus_sp._Nevada_1, 18 Brachionus_plicatilis_1, 19 Brachionus_plicatilis_2, 20 Brachionus_plicatilis_3, 21 Brachionus_plicatilis_4, 22 Brachionus_rotundiformis_1, 23 Brachionus_rotundiformis_2, 24 Brachionus_sp._Tiscar_1, 25 Brachionus_sp._Tiscar_2, 26 Brachionus_sp._Cayman_1, 27 Brachionus_sp._Cayman_2, 28 Brachionus_ibericus_1, 29 Brachionus_ibericus_2, 30 Brachionus_ibericus_3, 31 Brachionus_ibericus_4, 32 Brachionus_sp._Almenara_1, 33 Brachionus_sp._Almenara_2, 34 Brachionus_calyciflorus_1, 35 Brachionus_calyciflorus_2, 36 Brachionus_calyciflorus_3, 37 Brachionus_calyciflorus_4, 38 Brachionus_calyciflorus_5, 39 Brachionus_sessilis_Doirani_1, 40 Brachionus_sessilis_Doirani_2, 41 Brachionus_sessilis_Doirani_3, 42 Brachionus_sessilis_Doirani_4, 43 Brachionus_sessilis_Doirani_5, 44 Brachionus_sessilis_Balaton_1, 45 Brachionus_sessilis_Balaton_2, 46 Brachionus_rubens_1, 47 Brachionus_rubens_2, 48 Brachionus_rubens_3, 49 Brachionus_urceolaris, 50 Brachionus_leydigii, 51 Brachionus_quadridentatus_1, 52 Brachionus_quadridentatus_2; TREE PAUP_1 = (1:126.0,((((2:83.0,((3:8.0,4:6.0):40.0,(5:16.0,(6:0.0,7:1.0):7.0):29.0):74.0):53.0,(34:45.0,(35:12.0,((36:9.0,38:8.0):2.0,37:25.0):16.0):14.0):38.0):45.0,((((9:0.0,10:0.0):25.0,11:29.0):23.0,((((12:5.0,13:34.0):16.0,(17:2.0,(19:0.0,21:1.0):6.0):10.0):12.0,(14:0.0,(15:1.0,16:0.0):2.0):11.0):22.0,(18:1.0,20:4.0):26.0):23.0):14.0,((22:8.0,23:26.0):16.0,(((24:0.0,25:0.0):5.0,(26:1.0,27:2.0):16.0):13.0,((((28:9.0,33:19.0):13.0,31:5.0):10.0,(29:0.0,30:0.0):1.0):5.0,32:19.0):6.0):21.0):14.0):42.0):24.0,((((((39:0.0,40:0.0,41:0.0,42:0.0):1.0,43:0.0,44:0.0,45:0.0):31.0,(46:17.0,47:0.0):61.0):29.0,48:25.0):42.0,(50:30.0,(51:3.0,52:1.0):23.0):25.0):24.0,49:52.0):39.0):46.0,8:83.0); TREE PAUP_2 = (1:126.0,((((2:83.0,((3:8.0,4:6.0):40.0,(5:16.0,(6:0.0,7:1.0):7.0):29.0):74.0):53.0,(34:45.0,(35:12.0,((36:9.0,37:27.0):2.0,38:6.0):16.0):14.0):38.0):45.0,((((9:0.0,10:0.0):25.0,11:29.0):23.0,((((12:5.0,13:34.0):16.0,(17:2.0,(19:0.0,21:1.0):6.0):10.0):12.0,(14:0.0,(15:1.0,16:0.0):2.0):11.0):22.0,(18:1.0,20:4.0):26.0):23.0):14.0,((22:8.0,23:26.0):16.0,(((24:0.0,25:0.0):5.0,(26:1.0,27:2.0):16.0):13.0,((((28:9.0,33:19.0):13.0,31:5.0):10.0,(29:0.0,30:0.0):1.0):5.0,32:19.0):6.0):21.0):14.0):42.0):24.0,((((((39:0.0,40:0.0,41:0.0,42:0.0):1.0,43:0.0,44:0.0,45:0.0):31.0,(46:17.0,47:0.0):61.0):29.0,48:25.0):42.0,(50:30.0,(51:3.0,52:1.0):23.0):25.0):24.0,49:52.0):39.0):46.0,8:83.0); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1409660586836; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7699054737899036993; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5354287928439190714; mqVersion 275; checksumv 0 3 113277272 null getNumChars 428 numChars 428 getNumTaxa 52 numTaxa 52 short true bits 15 states 15 sumSquaresStatesOnly 452579.0 sumSquares 452579.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1 errorReportedDuringRun; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 373; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1600 764; setLocation -9 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #7699054737899036993 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #7699054737899036993; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; getTable; tell It; rowNamesWidth 153; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1227 697; setLocation -9 0; 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.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #7699054737899036993 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 3; toggleUseWeights off; endTell; setAssignedID 3583.1409660435502.6364829584410542382; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1227 697; setLocation -9 0; 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 on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; 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 1; 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; toggleWhiteEdges on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings; tell It; setOn on; 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 #5354287928439190714 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1227 697; setLocation -9 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; 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; toggleShowPaleGrid off; toggleShowPaleCellColors off; togglePaleInapplicable on; toggleShowBoldCellText 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.charMatrices.SelSummaryStrip.SelSummaryStrip; tell It; showStrip off; 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; endTell; end;