#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 18, 2025; 21:22 GMT

TreeBASE (cc) 1994-2008

Study reference:
Rodriguez-prieto A., Igea J., & Castresana J. 2014. Development of rapidly evolving
intron markers to estimate multilocus species trees of rodents. PLOS ONE, 9:
e96032.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S15064]

BEGIN TAXA;
        TITLE  Taxa;
        DIMENSIONS NTAX=15;
        TAXLABELS
            Apodemus_flavicollis
            Atherurus_macrourus
            Cavia_porcellus
            Cynomys_ludovicianus
            Glis_glis
            Homo_sapiens
            Hydrochoerus_hydrochaeris
            Microtus_duodecimcostatus
            Microtus_lusitanicus
            Mus_musculus
            Myocastor_coypus
            Octodontomys_gliroides
            Proechimys_guairae
            Rattus_norvegicus
            Sciurus_vulgaris
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M19792]

	TITLE 'Mammal Dhcr24-intron-7';
	LINK TAXA = Taxa;
	DIMENSIONS NCHAR=254;
	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       180       190       200       210       220       230       240       250       ]
[                                      .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .       ]
Apodemus_flavicollis          GTAAGCGGGCATGGTCCCAGGGAACCCAGGCCTTCTCCCTAGAGCTGTGTCACCCACCCATCTTTGTGTATCTGCCCTCTGGGCCTCGGTTTCTCCAAGTTCACAATTAGGGGTCTTGGCCACTCGGACCGAGTGTCCTGATAAGC--------TGGGAGTGTCTGAGTGGGGTGCAGAGTTGCGGGATGTGGGTGAACTAGCTCTGCTACCTGCTGGGAAAAGACAGGCCG-ACCTGTTTCTCTGACCTCTCA
Atherurus_macrourus           GTGAGCAGGCGCGGTCC{AG}GGGAC-TTCACAGTCTCTCCCCTGAGCC------CACGCCCACCCAGTCGCACCGGCCCTCTCAGCCG----------------------------------CTTGGCAGTGGAGCATTTCTCTGAACTGCTCCCGTGGTGGAGTCAGAGGAGGCGGCAGAGTGCGGGAGGCTGGGAG------------TGTCTGCTGGCGAAGAGGCACCAACGCCTGCCTCGCCGGCTTCCCC
Cavia_porcellus               GTGAGCAGGCGTGGCCCCAGGAC-TTCACAGCCTCTCCCCTGAGCC-CACAGCCCACCT-GCTGGGCCTGTCTGCCCTCTCGGCCTCAGTTTTTCCAACTGTAAAGTCAGGCTTTGTCCCCTTGGCAGTGGAGCACCTCTGTGAACAGCTCCTGTGGGGGCATCAGAGCAGA--GCAGGGTGTGGGAGGGTGGAAG---------TGTCACCTGCCCAAGAAGAGGCACCATTGCCCACCTGGCCGGCCTCCCC
Cynomys_ludovicianus          GTGAGCGGGCGGGGTCCCACCGAATCCCCAA-GTCTTGTCTAAGCCACATGCCCCACTT----TGACAGGCCTGCCCTCTGGGCCTCACCTTCCCCAACTACAAAATGGGGGGCTCGTCCCTCAGCGATGGAGCACCTCTGTGGACCACTCGGGTGGGGGAGTCAGAGTCTTAGGCAGGA----GGAGGGGGCGGGCTACAGCCCTGTCACCTGCTGGAGAAAAAGCACCAATACCCTCCTCCCTGGCCTCCTT
Glis_glis                     GTGAG---------TCCC-------------CGTCCCCTCTGAACT--GTGCCCCACCT----CCACAGGCCTGCC--GCAGGGCCTCATCTTCCCAACCGTAAACCAAGGGCCTGTCCC-----------GGCACTTCCATGGACTGTTCCAGTGGTGGAGTTGGAGGATACTGCAGAGTTGGGGATGGGGGACAGCCATGCCCTGCCACCTACTGGAGAAGTAGCTCCAATGCCTGCCTCCTTGTCCCCCC-
Homo_sapiens                  GTGAGCAGGTGCATTCCCTTGGAATCCATGGCTCCTCCCCTGAACCGTGTGACCGACCT----TGGGCACACTGCCCTCTGGGT----GTTTTCCCAACTTTAAGATGAGGTCCTTGTCCCTCAGTGATGGAGCACTCCCATGACCTGCTCCGATGGTGGAGTCAGAGAATGCTGCAAAGTGGGTGGGTATGAGCGGGCCAGCCCTGTCACCTGTTGGAGAAAAAGCACCAATACCCACCTCCCTGGTCTACCC
Hydrochoerus_hydrochaeris     GTGAGCAGGCATGGCCCCAGCAC-TTCGCAGCCTTT--CCTGAGCC--ACAGCCCACCT-GCTGG--------GCCCTGTCAGCCTCCGTTTTTCCAACTGTAAAATCAGGCTTTGTCCCCTTGGCAGTGGAGTACCTCTATGAATGGGTGCTGTGGTGGCATCAGAGCAGA--GCAGGGTGTGGGAGGGGGGGAG---------TGTCACCTGCCCCAGAAGAGGCTCCATTGCCCACCTCGCCGGCCTCCCC
Microtus_duodecimcostatus     GTAAGCGGGCATGCTCCCATGGGACCCAGACCTCCTCTCCAGAGCCATGT----CACCCAGCTTTGTGTATCTGCCCTCCGGGCCTCAGTTCCTCCAACCATAAAATGAGGATCTTAGCCCTCAGCCAGGGAAGGGTCTGATGGGCTGCT--GGTAGGAGTATCTGCGAGAGCTGCAAACTGGTGGAATGTGGGCAGGCCAGTCCT{CG}CTACCTG------------AGACCA-ACCCACTTCCCTGGCCTCTCA
Microtus_lusitanicus          GTAAGC{AG}GGCATGCTCCCATGGGACCCAGACCTCCTCTCCAGAGCCATGT----CACCCAGCTTTGTGTATCTGCCCTCCGGGCCTCAGTTCCTCCAACCATAAAATGAGGATCTTAGCCCTCAGCCAGGGAAGGGTCTGATGGGCTGCT--GGTAGGAGTATCTGCGAGAGCTGCAAACTGGTGGAATGTGGGCAGGCCAGTCCTGCTACCTG------------AGACCA-ACCCACTTCCCTGGCCTCTCA
Mus_musculus                  GTAAGCGGGCGTGGTCCCATGGAACCCAGGTCTTCTCCCTAGCTCTGTGTCGCCCACCCATC--TGTGTATCTGCCCTCTGGGCCTTGGTTTCTCCAACTATACAATTAGGATCTTAGCCCCCAGGAACTGAGTACCCTGATAAGCTGCTTTAGTGGAAGTATTTGAGTGGGTTACAAAGTGCAAGGATGTGGGTGAGCTAGTCCTGCTACCTGCTGGGAAAAGACAGACCA-AGCTGTTTCTCTGACCTCTCA
Myocastor_coypus              GTGAGCAGACCTGGCCCTGGGACATCCGTGGCCTCT-CCCTGATCC-CATAGCTCACCTGGGCAGATATGCCTGCCCTCTCAGCCTCAGTTTGGCCCAGTGTAAAATCAGGCCTTGTCCCCTTGGCAGCAGAGCATGTATCTGAAGGGCTCCTGTGGCGGCCTCAGAGCAG---GCAGGGTGTGGGAGGGTGAGAA---------TGACGCCTGCTGGAGAAGAGGTGCCAGTGCCCACCTCGCTGCCCTCCCC
Octodontomys_gliroides        GTGAGCAGGCCTGGCTCCGGGACATTGACAGCCTCTCCCCTGAGCC-CATAGCCCACCTGGCCAGGCATGCCTGTCCTCTCAGCTTCAGTTTGGCCAACTGTAAAATCAGGCCTTGTCCCCTTGGCAGTGGAGCATGTGTCTGAATGTCTCCTGTGGCAGTCTCAGAGCAG---GCA-GGTGTGGGAGGGTGGGAA---------TGGCACCTGCTGGAGAAGAGGCACCAGTGCCCACCTCGCCGGCCTCCCC
Proechimys_guairae            GTGAGCAGGCCTGGCCCCGGGACATTCATGGCCTCT-GCCTGATCC-CGTAGCTCACTAGGGCAGGCATGCCTGCCCCCTCAGCCTCAGTTTGGCCCAGTGTAAAATCAGGCCTTGTCCCCTTGGCAGCAGAGCGTGTGTCTAGGTGTGCTGAGTG----------AGCAGGCGGCAGGGTGGGGGAGGGTGAGGA---------TGACACCTGTTGGAGAAGAGGTGCCAGTGCCCACCTTGCTGGCCTCCCC
Rattus_norvegicus             GTAAGTGGGCATGGTCCCATGGAACCCAGGCCTTCTCCCTTGAGCTGTGTCACCCACCCATCTTTGTGTATCCGCCCTCTGGGCCTCAGTTTCTCCAGCTGTATGATTAGGGTCTTGCCTCTCTGGGACCAAGTGCCCTGATAAGCTGCTTCTGTGGGGGTATCTAAGTGAGTTACAAAGTTGTGGGATGTGGATGATTTAGTCCTGCTGCCTGCTGAGAAAAAATAGACCA-ACCTGTTTCTCTGACCTCCCA
Sciurus_vulgaris              GTGAGCAGGCGGGGTCCCACCAAATTCCCAG--TCTTCTCTGAGTCACATGCCCCACTT----CAGCAGGCCTGTCCTGTGGGCCTCACTTTCCCCACCTATAAAATGGGGCCTCAGCCCCTCAGTGATGG-GTTCCTCTGTGGACTGCTTCGGTGGGGGAGGCGGGGTGTCAACCAGGG----GGAGTGGGTGGGCTGCAGCCCTGTCA-CTGCGGGAGGAAAAGCACCAATGCCCTCCTCCCTGGCCTCCCC
;
END;