#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 20, 2025; 2:26 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:M19797]

	TITLE 'Mammal Trpv-intron-8';
	LINK TAXA = Taxa;
	DIMENSIONS NCHAR=184;
	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    ]
[                                      .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .    ]
Apodemus_flavicollis          GTGAGTGCATGGCCCCAGTGCCACCTGCCTGCCCAGTTCACCCCTTGCTCTCCCTCCTCCCCTGCCTCCAGTCTGGCTTCTATTCCCTCCTTCACTCTGCTTCCTTCCCTTCTG----CTCCCCG----TCCTCCCCCAACTGCTCCAGGCTCCATATTCCTCCCACTGTCTCTTCTCTTCCAG
Atherurus_macrourus           GTGAGTCCTTGGCGCCGATGCCACCTGCCCTGCCTGGCCTCCTCCTATTTTCCTTCTCTGCTCTTTCCCAACAAAGAGCCCATTGTCCCTGCTATTCTGCCTCCCTCTCTTCTAGTCCTTCCTCTCTCCCCTCCTCTCTCTCCCTCCTGGCCCCAGCCCTGTCACGCCTGC---CCCCTTCCAG
Cavia_porcellus               GTGAGTGCCTGGCCCTCCTGCAGCCG--CTGCCCAGCCCTCCTCCTCATCTCCTCCGAGTCATCCTGCCAGCAAAGAATCCATTGCCTCTCCTACTCTGCCT------------------------TCCTCTCCTCTCTTCTCCTCGGGGTTCCGCCGCTGTCACGCCCGCTCTCCTCTTCCAG
Cynomys_ludovicianus          GTGAGTGCTTGGTCCCCGCGCCACCAGCCCGCCCGGCCTCCCTCCTCCTCCAATTCCAGGTTCTCTTCCAACCAAGAGCCCATGTCCTCACATGCTCCGCCTCCCTCTCTTCTGTGCCTCCCTCTCTCCTGTCCTCTACCTTCTTCCCTGATCCACCTGCCACGGGCCCCCTCCCCTCTTTCAG
Glis_glis                     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Homo_sapiens                  GTAAGTGCCTGGCCCCCGTGCCCCCCACCCTGCCTGCCCTCCCCACGTTCTCCATCTCTGCTTTTTTCCAGGAAAGAGTCCTTTGTCTACCAGCCTCTGCCTCCCTCTCTTCTATCCCTTTCTCTCTCTCCTCCTCTCCTCTCCTGCTGGCCCCACCCCTTTCACGCCCCCTCCTGTCTTCCAG
Hydrochoerus_hydrochaeris     GTGAGTGCGTGGCCCCGATGCCAGCC-----CCTGCCCACCCTCCTGTTTTCCTTCTCTGCTCTTTCCCAATAAAGAATCCATTGCCTCTCCTATTCTGCCTCCTTCTCTGTT-----CTTTCCTCTCCTCTCCTCTGTTCTCCTCCTGGTTCCACCCCCATCACGCCTGCTGTTCTCTTCCAG
Microtus_duodecimcostatus     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Microtus_lusitanicus          ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Mus_musculus                  GTGAGTGCTTGGCCCCAGTGCCACCTGCCTACCCAGTTCTCCTCTTGCTCTCCCTCTTCCCCTCCCTCCAGTCTGACTTCTATTCTCTCCTTCACTCTGCTTCCTTCCCTTTTGTCCCTTCTCCA----TCCTCCCCCAACTCCTCCTGACTTGATATTCCTCCCACCGTCTCTTCTGTTCCAG
Myocastor_coypus              ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Octodontomys_gliroides        GTGAGTGCATGGCCCCGATGCCACCCACCCTCCTGTCCCGCCTCCTCTTTTCCTTCTCTGTGCTGTCC-------------ATTGT--------CTCTGTCTCCCTCTCTTCTATTCTTCCCTCTCTCCTCGCCTCTGTCCTACTCCTGGTTACGCCCCTGTCACGCCTGCTGTCGTCTTCCAG
Proechimys_guairae            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Rattus_norvegicus             GTGAGTGCTTGGCCCCAGAGCCAGCTGCCTGCCAAGTTCCCTTCCTCCTCTCCCTCCCCTCCCCTCCCCAGTCTGGCTTCTATTCT-TCCCTCACTCTGTTCCCTTCCCTTCTGTCCCTTCCCCG----TCCTCCCCCAACTCCTCCTGGCTCCATATTCCTCTCACCGTCTCTTCTCTTCCAG
Sciurus_vulgaris              GTGAGTGCTTGGCCCCCGAGCCACCAG-CTGCCCGGCCTCCCTCCTGCTCCAATCCTGTGTTCTCTTCCAGCCAAGAGCCCAGGTCCTCCCGTGCTCTGCCTCCCTCTCCTCTGTCCCTTCCTCTCTCCTGCCCTCGACCTTCTTCCTGGCTCCACCTGTCACGGGCTCCCTCCCCTCCTTCAG
;
END;