#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 18, 2024; 23:10 GMT TreeBASE (cc) 1994-2008 Study reference: Honma H., Suyama Y., & Nakai Y. 2011. Detection of parasitizing coccidia and determination of host crane species, sex and genotype by faecal DNA analysis. Molecular Ecology Resources, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S11586] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=42; TAXLABELS Balearica_pavonina Balearica_pavonina_regulorum Grus_americana Grus_antigone Grus_canadensis Grus_carunculatus Grus_grus Grus_japonensis 'Grus japonensis Akan-1' 'Grus japonensis OK-1' 'Grus japonensis OK-2' 'Grus japonensis OK-3' 'Grus japonensis OK-4' 'Grus japonensis OK-5' 'Grus japonensis OK-6' 'Grus japonensis OK-7' Grus_leucogeranus Grus_monacha 'Grus monacha IPZ-2' 'Grus monacha IPZ-3' 'Grus monacha IPZ-4' 'Grus monacha IPZ-5' 'Grus monacha Izumi-1' 'Grus monacha Izumi-2' 'Grus monacha Izumi-3' 'Grus monacha Izumi-6' 'Grus monacha Izumi-7' Grus_nigricollis 'Grus nigricollis UZ-1' 'Grus nigricollis UZ-2' 'Grus nigricollis UZ-5' 'Grus nigricollis UZ-7' Grus_paradisea Grus_rubicunda Grus_vipio 'Grus vipio Izumi-4' 'Grus vipio Izumi-5' 'Grus vipio Izumi-8' 'Grus vipio UZ-3' 'Grus vipio UZ-4' 'Grus vipio UZ-6' Grus_virgo ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M9083] TITLE Grus_Mt_16S_alignment; LINK TAXA = Taxa1; DIMENSIONS NCHAR=146; 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] [ . . . . . . . . . . . . . . . . .] Balearica_pavonina GCTAAAATAAGTACTAGGGTTCCCTCGAGCGCAAGCTTACATCATCACATTATTAACAGACTACAGCTAATGTTGAAACTAACAAGACTAAACATTAAACACCCTGTTAACCCAACCCAGGTGCGCCCATTAGAAAGATTAAAACC Balearica_pavonina_regulorum GCTAAAATAAGTACTAGGGCCCCCTCAAGCGCAAGCTTACATTATCACATTATTAACAGACTACAGCTAATGTCGAAACTAACAAGACTAAGCATTAAACACCCTGTTAACCCAACCCAGGGGCGCCCATTAGAAAGATTAAAACC Grus_americana GCTAAAATAAGTACTGGGGCACCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAATGCTGCAACCAACAAGACTAAACATTAAACACCCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC Grus_antigone GCTAAAATAAGTACTAGGGTTCCCTCAAGCGCAAGCTTACATCACTACATTATTAACAGACCACGGCTAATGCCGCAGCCAACAAGACCAAACATTAAACACCCTGTTAACCCAACTCAGGAGCGCTTATTAGAAAGATTGAAACC Grus_canadensis GCTAAAATAAGTACTAGGGTTCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCGCGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACCCTGTTAACCCGACTCAGGAGCGCTTATCAGAAAGATTAAAACC Grus_carunculatus GCTAAAATAAGTACTAGGGCTCCCTCAAGCGCAAGCTTACATCACTACATTATTAACAGACCACAGCTAATGCTGCAACCAACAAGACCAAACATTAAACACCCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGACTAAAGCC Grus_grus GCTAAAATAAGTACTAGGGCACCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACTACGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACCCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC Grus_japonensis GCTAAAATAAGTACTAGGGCCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCGCGACTAATGCTGCAACCAACAAGACCAGACATTAAACACCCTGTTAACCCAACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus japonensis Akan-1' GCTAAAATAAGTACTAGGGCCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCGCGACTAATGCTGCAACCAACAAGACCAGACATTAAACACCCTGTTAACCCAACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus japonensis OK-1' GCTAAAATAAGTACTAGGGCCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCGCGACTAATGCTGCAACCAACAAGACCAGACATTAAACACCCTGTTAACCCAACTCAGGAGCGCTTATTA{AG}AAA{AG}ATTGAAACC 'Grus japonensis OK-2' GCTAAAATAAGTACTAGGGCCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCGCGACTAATGCTGCAACCAACAAGACCAGACATTAAACACCCTGTTAACCCAACTCAGGAGCGCTTATTA{AG}AAA{AG}ATTGAAACC 'Grus japonensis OK-3' GCTAAAATAAGTACTAGGGCCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCGCGACTAATGCTGCAACCAACAAGACCAGACATTAAACACCCTGTTAACCCAACTCAGGAGCGCTTATTA{AG}AAA{AG}ATTGAAACC 'Grus japonensis OK-4' GCTAAAATAAGTACTAGGGCCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCGCGACTAATGCTGCAACCAACAAGACCAGACATTAAACACCCTGTTAACCCAACTCAGGAGCGCTTATTA{AG}AAAGATTGAAACC 'Grus japonensis OK-5' GCTAAAATAAGTACTAGGGCCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCGCGACTAATGCTGCAACCAACAAGACCAGACATTAAACACCCTGTTAACCCAACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus japonensis OK-6' GCTAAAATAAGTACTAGGGCCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCGCGACTAATGCTGCAACCAACAAGACCAGACATTAAACACCCTGTTAACCCAACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus japonensis OK-7' GCTAAAATAAGTACTAGGGCCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCGCGACTAATGCTGCAACCAACAAGACCAGACATTAAACACCCTGTTAACCCAACTCAGGAGCGCTTATTAGAAAGATTGAAACC Grus_leucogeranus GCTAAAATAAGTACTAGGATTTCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACTGTGACTAATGCTGCAACCAACAAGACCAAACATTAAACACCCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC Grus_monacha GCTAAAATAAGTACTAGGGTCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACTCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus monacha IPZ-2' GCTAAAATAAGTACTAGGGTCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACTCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus monacha IPZ-3' GCTAAAATAAGTACTAGGGTCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACTCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus monacha IPZ-4' GCTAAAATAAGTACTAGGGTCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACTCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus monacha IPZ-5' GCTAAAATAAGTACTAGGGTCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACTCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus monacha Izumi-1' GCTAAAATAAGTACTAGGGTCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAA?GCTGCAACCAACAAGACCAAACATTAAACACTCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus monacha Izumi-2' GCTAAAATAAGTACTAGGGTCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACTCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus monacha Izumi-3' GCTAAAATAAGTACTAGGGTCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACTCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus monacha Izumi-6' G?TAAAATAAGTACTAGGGTCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAA????GCAACCAACAAGACCAAACATTAAACACTCTGTTAACCCGACTCA?GAGCGC??ATTAGAAAGATTGAAACC 'Grus monacha Izumi-7' GCTAAAATAAGTACTAGGGTCCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACTCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC Grus_nigricollis GCTAAAATAAGTACTAGGGTTCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACTCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus nigricollis UZ-1' GCTAAAATAAGTACTAGGGTTCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACTCTGTTAACCC{AG}ACTCAGGAGCGCTTATTA{AG}AAAGATTGAAACC 'Grus nigricollis UZ-2' GCTAAAATAAGTACTAGGGTTCCCTCAAGCGCAAGCTTACATCATTACATTATTAACAGACCACGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACTCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus nigricollis UZ-5' GCTAAAATAAGTACTAGGGTTCCCTCAAGCGCAAGCTTACATCATTACATTATTAACA{AG}ACCACGGCTAATGCTGCAACCAACAA{AG}ACCAAACATTAAACACTCTGTTAACCCGACTCAGGAGCGCTTATTA{AG}AAA{AG}ATTGAAACC 'Grus nigricollis UZ-7' GCTAAAATAAGTACTAGGGTTCCCTCA{AG}GCGCAAGCTTACATCATTAC{AT}TTATTAACAGACCACGGCTAATGCTGCAACCAACAAGACCAAACATTAAACACTCTGTTAACCCGACTCAGGAGCGCTTATTA{AG}AAAGATTGAAACC Grus_paradisea GCTAAAATAAGTACTAGGGCTCCCTCAAGCGCAAGCTTACATTATTACATTATTAACAGACCACGGCCAATGCTACAACCAACAAGACCAAACATTAAACACCCTGTTAACCCGACTCAGGAGCGCTTGTTAGAAAGATTGAAACC Grus_rubicunda GCTAAAATAAGTACTAGGGCTCCCTCAAGCGCAAGCTTACATCACTATATTATTAACAGACCACGGCTAATGCCACAACCAACAAGACCAAACATTAAACATCCTGTTAACCCGACCCAGGAGCGCTTATTAGAAAGATTGAAACC Grus_vipio GCTAAAATAAGTACTAGGGTTCCCTCAAGCGCAAGCTTACATCACTACATTATTAACAGACCTCGGCTAATGCCACAACCAACAAGACCAAACATTAAACACCCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus vipio Izumi-4' GCTAAAATAAGTACTAGGGTTCCCTCAAGCGCAAGCTTACATCACTACATTATTAACAGACCTCGGCTAATGCCACAACCAACAAGACCAAACATTAAACACCCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus vipio Izumi-5' GCTAAAATAAGTACTAGGGTTCCCTCAAGCGCAAGCTTACATCACTACATTATTAACAGACCTCGGCTAATGCCACAACCAACAAGACCAAACATTAAACACCCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus vipio Izumi-8' GCTAAAATAAGTACTAGGGTTCCCTCAAGCGCAAGCTTACATCACTACATTATTAACAGACCTCGGCTAA?GCCACAACCAACAAGACCAAACATTAAACACCCTGTTAACCCGACTCAGGAGCGCTTATTAGAAAGATTGAAACC 'Grus vipio UZ-3' GCTAAAATAAGTACTAGGGTTCCCTCAAGCGCAAGCTTACATCACTACATTATTAACAGACCTCGGCTAATGCCACAACCAACAAGACCAAACATTAAACACCCTGTTAACCC{AG}ACTCAGGAGCGCTTATTA{AG}AAAGATTGAAACC 'Grus vipio UZ-4' GCTAAAATAAGTACTAGGGTTCCCTCAAGCGCAAGCTTACAT{AC}A{CT}TA{CT}ATTATTAACA{AG}ACCTCGGCTAATGCCACAACCAACAA{AG}ACCAA{AT}CATTAA{AC}CACCCTGTTAACCCGACTCAGGAGCGCTTATTA{AG}AAAGATTGAAACC 'Grus vipio UZ-6' GCTAAAATAAGTACTAGGGTTCCCTCAAGCGCAAGCTTACAT{AC}ACTACATTATTAACA{AG}ACCTCGGCTAATGCCACAACCAACAA{AG}ACCAAACATTAAACACCCTGTTAACCCGACTCAGGAGCGCTTATTA{AG}AAA{AG}ATTGAAACC Grus_virgo GCTAAAATAAGTACTAGGGCTCCCTCAAGCGCAAGCTTACATTATTACATTATTAACAGACCACGGCCAATGCTACAACCAACAAGACCAAACATTAAACACCCTGTTAACCCAACTCAGGAGCGCTCGTTAGAAAGATTGAAACC ; END; BEGIN TREES; TITLE Grus_16S_Result; LINK TAXA = Taxa1; TRANSLATE 1 'Grus japonensis Akan-1', 2 Balearica_pavonina, 3 Balearica_pavonina_regulorum, 4 Grus_americana, 5 Grus_antigone, 6 Grus_canadensis, 7 Grus_carunculatus, 8 Grus_grus, 9 Grus_japonensis, 10 Grus_leucogeranus, 11 Grus_monacha, 12 Grus_nigricollis, 13 Grus_paradisea, 14 Grus_rubicunda, 15 Grus_vipio, 16 Grus_virgo, 17 'Grus monacha IPZ-2', 18 'Grus monacha IPZ-3', 19 'Grus monacha IPZ-4', 20 'Grus monacha IPZ-5', 21 'Grus monacha Izumi-1', 22 'Grus monacha Izumi-2', 23 'Grus monacha Izumi-3', 24 'Grus vipio Izumi-4', 25 'Grus vipio Izumi-5', 26 'Grus monacha Izumi-6', 27 'Grus monacha Izumi-7', 28 'Grus vipio Izumi-8', 29 'Grus japonensis OK-1', 30 'Grus japonensis OK-2', 31 'Grus japonensis OK-3', 32 'Grus japonensis OK-4', 33 'Grus japonensis OK-5', 34 'Grus japonensis OK-6', 35 'Grus japonensis OK-7', 36 'Grus nigricollis UZ-1', 37 'Grus nigricollis UZ-2', 38 'Grus vipio UZ-3', 39 'Grus vipio UZ-4', 40 'Grus nigricollis UZ-5', 41 'Grus vipio UZ-6', 42 'Grus nigricollis UZ-7'; TREE Fig._2 = [&R] ((2:0.018126,3:0.039319):0.055028,(7:0.028306,((4:0.014679,8:0.006888):0.009503,((6:0.01423,(10:0.030433,(35:0.0,(1:0.0,(33:0.0,(32:0.0,(29:0.0,(30:0.0,(31:0.0,(9:0.0,34:0.0):0.0):0.0):0.0):0.0):0.0):0.0):0.0):0.030441):0.00633):0.006932,(((14:0.036224,(13:0.0,16:0.014261):0.029218):0.00419,(41:0.0,(39:0.0,(25:0.0,(24:0.0,(28:0.0,(15:0.0,38:0.0):0.0):0.0):0.0):0.0):0.0):0.018243):0.0116,(5:0.029224,((42:0.0,(40:0.0,(37:0.0,(12:0.0,36:0.0):0.0):0.0):0.0):0.0,(27:0.0,(26:0.0,(20:0.0,(19:0.0,(17:0.0,(18:0.0,(22:0.0,(21:0.0,(11:0.0,23:0.0):0.0):0.0):0.0):0.0):0.0):0.0):0.0):0.0):0.006948):0.007009):0.0):0.0):0.005346):0.011388):0.055028); END;