#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; 2:41 GMT TreeBASE (cc) 1994-2008 Study reference: Sasaki T., Yasukawa Y., Takahashi K., Miura S., & Okada N. 2006. Extensive Morphological Convergence and Rapid Radiation in the Evolutionary History of the family Geoemydidae (Old World Pond Turtles) Revealed by SINE Insertion Analysis. Systematic Biology, 55(6): 912-927. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1609] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=28; TAXLABELS Batagur_baska Callagur_borneoensis Cuora_amboinensis Cuora_mouhotii Emys_orbicularis Geochelone_carbonaria Geoemyda_spengleri Heosemys_annandalii Heosemys_grandis Kinixys_erosa Kinixys_homeana Malayemys_macrocephala Mauremys_annamensis Mauremys_japonica Mauremys_mutica_kami Mauremys_reevesii Mauremys_sinensis Melanochelys_trijuga Notochelys_platynota Orlitia_borneensis Pangshura_smithii Pyxis_arachnoides Rhinoclemmys_funerea Rhinoclemmys_punctularia_punctularia Sacalia_bealei Siebenrockiella_crassicollis Testudo_horsfieldii Trachemys_scripta_elegans ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2573] TITLE 'Appendix 2 - SINEs'; LINK TAXA = Taxa1; DIMENSIONS NCHAR=49; FORMAT DATATYPE=Standard SYMBOLS= "0 1" MISSING=? GAP= -; MATRIX [ 10 20 30 40 ] [ . . . . ] Batagur_baska 1?11111000001110000?00000?00000000?00011110000000 Callagur_borneoensis 1111111000001110000?00000000000000?00011110000000 Cuora_amboinensis 1111111000110000000100000000000000000010000000000 Cuora_mouhotii ?1111?10001100000?010000000000?00?000010000000010 Emys_orbicularis 000000000000?00000000000000?000000000000000000000 Geochelone_carbonaria 1111111111000000000?00000000000000000000010000000 Geoemyda_spengleri 111111100?110000000000000000000000000010000000000 Heosemys_annandalii 1111111000110000000011111000000001111110000000000 Heosemys_grandis 1111111000110000000011111000000001111110000000000 Kinixys_erosa 111?111111?000000000000000?0000000000000010000000 Kinixys_homeana 11111111110000000000000000??000000000000010000000 Malayemys_macrocephala 111?111000001100000000?000000000000000111?0000000 Mauremys_annamensis 1111111?00110001111000000000011110000010000000000 Mauremys_japonica 1111111000110001111000000111100000?00010000000000 Mauremys_mutica_kami 11?1111000110001111000000000011110000010000000000 Mauremys_reevesii 1111111000110001111000000110000000000010000000100 Mauremys_sinensis 111111100011?0011110000001111000?0000010000111000 Melanochelys_trijuga 11111?10001100000?0011111000000000000010000000001 Notochelys_platynota 1111111000110000000011111000000001110010000000000 Orlitia_borneensis 1111111000001100000000000000000000?00011110000000 Pangshura_smithii 111111100000111000??00000000000000000011111000000 Pyxis_arachnoides 111111111100?00000?000000000000?00000000010000000 Rhinoclemmys_funerea 11111110?0110000000000000000000000?00010000000000 Rhinoclemmys_punctularia_punctularia 11111110?0110000000000000000000?00??0010?00000000 Sacalia_bealei 111111100011000000?01111100?000001110010000000000 Siebenrockiella_crassicollis 1111?1100000000000000000?0000?0000000011100000000 Testudo_horsfieldii 11111?111100000000000?000000000000000000010000000 Trachemys_scripta_elegans 000000000000?000000000000?0?0000000??000000000000 ; END; BEGIN TREES; TITLE Tb7916; LINK TAXA = Taxa1; TRANSLATE 1 Testudo_horsfieldii, 2 Kinixys_erosa, 3 Kinixys_homeana, 4 Geochelone_carbonaria, 5 Pyxis_arachnoides, 6 Pangshura_smithii, 7 Callagur_borneoensis, 8 Batagur_baska, 9 Orlitia_borneensis, 10 Malayemys_macrocephala, 11 Siebenrockiella_crassicollis, 12 Mauremys_sinensis, 13 Mauremys_japonica, 14 Mauremys_reevesii, 15 Mauremys_mutica_kami, 16 Mauremys_annamensis, 17 Cuora_amboinensis, 18 Cuora_mouhotii, 19 Heosemys_annandalii, 20 Heosemys_grandis, 21 Sacalia_bealei, 22 Notochelys_platynota, 23 Melanochelys_trijuga, 24 Geoemyda_spengleri, 25 Rhinoclemmys_punctularia_punctularia, 26 Rhinoclemmys_funerea, 27 Emys_orbicularis, 28 Trachemys_scripta_elegans; TREE Fig._2 = [&R] (((1,2,3,4,5)Testudinidae,((((6,7,8),9,10),11),((((12,13),14),(15,16))Genus_Mauremys,(17,18)Genus_Cuora,(((19,20),21,22),23),24,25,26)))Testuguria,27,28); END;