#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 September 19, 2025; 0:31 GMT TreeBASE (cc) 1994-2008 Study reference: Van dijk M., Paradis E., Catzeflis F., & De jong W. 1999. The virtues of gaps: Xenarthran (Edentate) monophyly supported by a unique deletion in alphaA-crystallin. Systematic Biology, 48(1): 94-106. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S604] BEGIN TAXA; TITLE HKY_model_ML; DIMENSIONS NTAX=39; TAXLABELS Anas_platyrhynchos Bos_taurus Bradypus_tridactylus Cabassous_unicinctus Cebus_albifrons Choloepus_didactylus Colobus_guereza Columba_livia Crotophaga_sulcirostris Cyclopes_didactylus Dasypus_novemcinctus Didelphis_marsupialis Eudromia_elegans Galago_crassicaudatus Gallus_gallus Homo_sapiens Leontopithecus_rosalia Lophura_nycthemera Loxodonta_africana Macaca_mulatta Macropus_rufus Mesocricetus_auratus Mus_musculus Opisthocomus_hoazin Oryctolagus_cuniculus Pan_troglodytes Propithecus_sp. Pteropus_hypomelanus Rana_catesbeiana Rana_temporaria Rattus_norvegicus Spalax_ehrenbergi Sterna_fuscata Tamandua_telradactyla Tarsius_syrichta Tonatia_silvicola Trachemys_scripta_elegans Tupaia_glis Turdus_merula ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M3925] TITLE 'alpha A-crystallin'; LINK TAXA = HKY_model_ML; DIMENSIONS NCHAR=145; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=N GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 ] [ . . . . . . . . . . . . . . ] Anas_platyrhynchos CCGCCGGTACCGCCTGCCCGCCAACGTGGACCAGTCTGCCATCACCTGCTCCCTCTCCGGCGACGGCATGCTGACCTTCTCAGGCCCCAAGGTCCCCTCCAACATGGACCCCACCCACAGCGAGAGGCCCATCCCCNNNNNNNNN Bos_taurus CCGCCGCTACCGCCTGCCTTCCAACGTGGACCAGTCCGCACTCTCCTGCTCCCTGTCCGCTGATGGCATGCTGACCTTCTCTGGCCCCAAGATCCCATCTGGCGTGGACGCCGGCCACAGCGAGCGGGCCATCCCCGTGTCCCGG Bradypus_tridactylus CCGCCGCTACCGCCTGCCCACGGCTGTGGACCAGTCTGCACTGTCCTGCTCCCTGTCGGCCGACGGCATGCTGACCTTCTCGGGCCCCAAGAT---------CGTGGACCCCAGCCACAGCGAGCGCCCCATCCCCGTGTCCCGG Cabassous_unicinctus CCGCCGCTACCGCCTGCCCACCGCCGTGGACCAGTCCGCGCTGACCTGCTCCTTGTCGGCCGACGGCATGCTGACCTTCTCTGGCCCCAAGAC---------CGTGGATCCCAGCCACAGCGAGCGGCCCATCCCTGTGTCCCGG Cebus_albifrons NNNNNNNNNNNNNNNNCCGTCCAACGTGGACCAGTCGGCCCTCTCTTGCTCCCTGTCCGCTGACGGCATGCTGACCTTCTCTGGCCCCAAGATCCAGACTGGCCTGGACACCACCCACGGCGAGCGAGCCATCCCCGTGTCGCGG Choloepus_didactylus CCGCCGCTACCGCCTGCCCACGGCCGTGGACCAGTCCGCGCTGTCCTGCTCCCTGTCGGCCGACGGCATGCTGACCTTCTCGGGCCCCAAGAT---------CGTGGACCCCAGCCACAGCGAGCGCACCATCCCCGTGTCCCGG Colobus_guereza NNNNNNNNNNNNNNNNCCGTCCAACGTGGACCAGTCGGCCCTCTCTTGCTCCCTGTCCGCCGATGGCATGCTGACCTTCTCTGGCCCCAAGATCCAGACTGGCCTAGATGCCACCCACG---AGCGAGCCATTCCCGTGGCGCGG Columba_livia CCGCCGGTACCGCCTGCCCGCCAACGTGGACCAGGCTGCCATCACCTGCTCCCTGTCCAACGACGGCATGCTGACCTTCTCGGGCCCCAAGGTCCCCGCCAACATGGACGCCAGCCACGGCGAGAGGCCCATCCCCNNNNNNNNN Crotophaga_sulcirostris CCGCCGGTACCGCCTGCCTGCCAACGTGGACCAGGCTGCCATCACCTGCTCCCTGTCGAACGACGGCATGCTGACCTTCTCGGGCCCCAAGGTTCCCTCCAACATGGACACCAGCCACGTCGAGAGACCCATCCNNNNNNNNNNN Cyclopes_didactylus CCGCCGCTACCGCCTGCCCACAGCCGTGGACCAGTCTGCGCTGTCCTGCTCCCTGTCGGCCGACGGCATGCTGACCTTCTCGGGCCCCAAGCT---------CGTGGACCCCAGCCACAGCGAGCGGGCCATCCCCGTGTCCCGG Dasypus_novemcinctus CCGCCGCTACCGCCTGCCGCCCTCGGTGGACCAGTCGGCGCTCTCCTGCTCCCTGTCGGCCGACGGCATGCTGACCTTCTCGGGCCCCAAGGC---------CGTGGAGCCCGGCCACGGCGAGCGGCCCATCCCCGTGTCCCGG Didelphis_marsupialis TCGCCGATACCGCCTGCCTTCCAATGTGGACCAGGCCTCCATTTCCTGCTCCCTGTCTGCTGATGGCATGCTGACCTTCTCTGGTCCCAAGATCCACTCTAACATGGAATCAAGCCACAGTGATCGGTCCATCCCTGTATCTCGT Eudromia_elegans CCGCCGGTACCGCCTGCCCTCCAACGTGGACCAGTCTGCCATCACCTGCTCCCTCTCCAGTGACGGCATGCTGACCTTCTCCGGCCCCAAGGTCCAGGCCAACATGGACCCCAGCCACAGCGAGAGACCCATCCCTNNNNNNNNN Galago_crassicaudatus NNNNNNNNNNNNNNNNCCTTCCAACGTGGACCAGTCGGCCCTGTCCTGCTCCGTGTCCGCAGACGGCATGCTGACATTCTCTGGCCCCAAGGTCCAGTCCGGCCTGGATGCCGGCCACAGCGAGCGAGCCATCCCCGTGTCGCGG Gallus_gallus CCGCCGGTACCGCCTGCCTGCTAACGTGGACCAATCCGCCATCACCTGTTCCCTGTCCAGCGACGGCATGCTGACCTTCTCGGGCCCAAAGGTCCCCTCCAATATGGACCCCAGCCACAGCGAGAGGCCCATCCCCGTGTCCCGG Homo_sapiens CCGCCGCTACCGCCTGCCGTCCAACGTGGACCAGTCGGCCCTCTCTTGCTCCCTGTCTGCCGATGGCATGCTGACCTTCTGTGGCCCCAAGATCCAGACTGGCCTGGATGCCACCCACGCCGAGCGAGCCATCCCCGTGTCGCGG Leontopithecus_rosalia NNNNNNNNNNNNNNNNCCGTCCAACGTGGACCAGTCGGCCCTGTCCTGCACCCTGTCCGCCGACGGCATGCTGACCTTCACTGGCCCCAAGATCCAGACTGGCCTGGACGCCACCCACGGCGAGCGAGCCATCCCCGTGTCGCGG Lophura_nycthemera CCGCCGGTACCGCCTGCCCGCCAATGTGGACCAGTCTGCCATCACCTGTTCCTTGTCCAGCGACGGCATGCTGACCTTCTCGGGCCCAAAGGTCCCTTCCAATATGGACCCCAGCCACAGCGAGAGGCCCATCCNNNNNNNNNNN Loxodonta_africana NNNNNNNNNNNNNNNNCCCTCCAACGTGGACCAGTCTGCACTCTCTTGCTCCCTGTCTGCGGACGGCATGCTGACCTTCTGTGGCCCCAAGATCCAGTCTGGCATGGATGCCAGCCACAGTGAGAGAGCCATCCCCGTGTCCCGG Macaca_mulatta NNNNNNNNNNNNNNNNNNNTCCAACGTGGACCAGTCGGCCCTCTCTTGCTCCCTGTCCGCCGACGGCATGCTGACCTTCTCTGGCCCCAAGATCCAGACTGGCCTAGACGCCACCCATG---AGCGAGCCATTCCCGTGGCGCGG Macropus_rufus TCGTCGATACCGTCTGCCTTCCAACGTGGATCAGGCCTCCATTTCCTGCTCCCTGTCTGCTGATGGCATGCTGACCTTCTCTGGTCCCAAGATCCACTCCAACATGGATGCAAGCCACAGTGATCGATCCATCCCTGTATCTCGT Mesocricetus_auratus CCGTCGCTACCGTCTGCCTTCCAATGTGGACCAGTCTGCCCTCTCCTGCTCCCTGTCTGCGGATGGCATGCTGACCTTCTCTGGCCCAAAGGTCCAGTCCGGCTTGGATGCTGGCCACAGTGAGAGGGCCATTCCTGTGTCACGG Mus_musculus CCGTCGCTACCGTCTGCCTTCCAATGTGGACCAGTCCGCCCTCTCCTGCTCCCTGTCTGCTGATGGCATGCTGACCTTCTCTGGCCCCAAAGTCCAGTCCGGTTTGGATGCTGGCCACAGCGAGAGGGCCATTCCTGTGTCACGG Opisthocomus_hoazin CCGCCGGTACCGCCTGCCCGCCAACGTGGACCAGGCTGCCATCAGCTGCTCCCTGTCCAGCGACGGCATGCTGACCTTCTCGGGCCCCAAGGTCCCCTCCAACATGGACGCCGGCCACGTCGAGAGGCCCATCCNNNNNNNNNNN Oryctolagus_cuniculus CCGGCGCTACCGCCTGCCTTCCAACGTGGACCAGTCGGCGCTGTCCTGCTCGCTCTCCGCGGACGGCATGCTCACCTTCTCCGGCCCCAAGGTGCAGTCCGGCCTGGACGCTGGCCACAGCGAGCGAGCCATCCCCGTGTCCCGG Pan_troglodytes NNNNNNNNNNNNNNNNCCGTCCAACGTGGACCAGTCGGCCCTCTCTTGCTCCCTGTCCGCCGATGGCATGCTGACCTTCTGTGGCCCCAAGATCCAGACTGGCCTGGATGCCACCCACGCCGAGCGAGCCATCCCCGTGTCGCGG Propithecus_sp. NNNNNNNNNNNNNNNNCCCTCCAACGTGGACCAGTCGGCGTTGTCCTGCTCCCTGTCCGCGGACGGCATGCTGACGTTCTCCGGCCCCAAGATCCCGTCTGGCCTGGACGCCGGCCACAGCGAGCGAGCCATCCCCGTGTCGCGG Pteropus_hypomelanus NNNNNNNNNNNNNNNNCCCTCCAACGTGGACCAGTCGGCGCTGTCCTGCTCCCTGTCCGCCGACGGCATGCTGACCTTCTCCGGCCCCAAGGTCCCATCTGGCGTGGACGCCGGCCACAGCGAGCGAGCCATCCCCGTGTCGCGG Rana_catesbeiana CCGCCGCTACCGCCTCCCCTCCAACCTGGACCAATCCTCTATCAGCTGCTCACTCTCTGCTGATGGCATTTTGACCTTCAGCGGACCAAAAATGATGTCAGGCCTGGACTCCAGCCACAGCGAGAGGCCTATCCCTGTGTCCAGA Rana_temporaria CCGCCGCTACCGCCTCCCCTCCAACCTGGACCAATCCTCTATCAGCTGCTCACTCTCTGCCGATGGCATTCTGACCTTCAGCGGACCAAAAATGATGTCAAACCTGGTCTCCAGCCACAGCGAGAGGCCCATCCCTGTGTCCAGA Rattus_norvegicus CCGTCGCTACCGTCTGCCTTCCAATGTGGACCAGTCCGCCCTCTCCTGCTCCTTGTCTGCGGATGGCATGCTGACCTTCTCTGGCCCCAAGGTCCAGTCTGGCTTGGATGCTGGCCACAGCGAGAGGGCCATTCCCGTGTCACGG Spalax_ehrenbergi CCGCCGATACCGCCTGCCTTCCAGTGTGGACCAGTCTGCCCTTTCCTGCTCCCTGTCTGCAGATGGCATGCTGACCTTCTCTGGCCCCAAAGTCCAATCTGGCCTGGATGCTGGCCACAGTGAAAGGGCCATTCCTGTGTCTCAG Sterna_fuscata CCGCCGGTACCGCCTGCCCGCCAACGTGGACCAGGCTGCCATCACCTGCTCCCTGTCCAACGACGGCATGCTGACCTTCTCTCGCCCCAAGGTCCCCGCCAACATGGACGCCAGCCACAGCGAGAGGCCTATCCNNNNNNNNNNN Tamandua_telradactyla CCGCCGCTACCGCCTGCCCACAGCCGTGGACCAGTCCGCGCTGTCCTGCTCCCTGTCGGCCGACGGCATGCTGACCTTCTCGGGCCCCAAGCT---------CGTGGACCCCAGCCACGGCGAGCGGACCATCCCCGTGTCCCGG Tarsius_syrichta NNNNNNNNNNNNNNNNCCGTCCAACGTGGACCAGTCGGCCCTCTCTTGCTCCCTGTCCGCCGATGGCATGCTGACCTTCTCTGGCCCCAAGATCCAGTCCGGCCTGGACGCCGGCCACAGCGAGCGAGCCATCCCCGTGTCACGG Tonatia_silvicola NNNNNNNNNNNNNNNNCCCTCCAACGTGGACCAGTCGGCCCTCTCTTGCTCCCTGTCAGCCGACGGCATGCTGACCTTCTCTGGCCCCAAGATCCAGTCTGGCCTGGACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Trachemys_scripta_elegans CCGCAGATACCGCCTGCCTTCCAACGTGGACCAATCTGCCATCACCTGCTCCCTGTCTGCTGATGGCATGCTGACTTTCTCTGGCCCAAAAGTCCAGTCCAACATGGACACCAGCTATAGCGAGAGACCCATTCCTNNNNNNNNN Tupaia_glis NNNNNNNNNNNNNNNNCCTTCCAACGTGGACCAGTCGGCCCTCTCCTGCTCCCTGTCAGCAGACGGCATGCTGACCTTCTCGGGCCCCAAGGTCCAGTCGGGCCTGGACGCTGGCCACAGCGAGCGACCCATCCCCGTGTCCCGA Turdus_merula CCGCCGCTACCGCCTGCCCGCCAACGTGGACCAGGCTGCCATCACCTGCTCCCTGTCCAACGATGGCATGCTGACCTTCTCGGGCCCCAAGGTCCCCTCCAACATGGACGCCAGCCACAGCGAGAGGCCCATCCNNNNNNNNNNN ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'alpha A-crystallin') = N: 1-145; CODONPOSSET CodonPositions (CHARACTERS = 'alpha A-crystallin') = N: 1-145; END;