#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; 7:32 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:M19791]

	TITLE 'Mammal Catsper3-intron-5';
	LINK TAXA = Taxa;
	DIMENSIONS NCHAR=303;
	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       260       270       280       290       300   ]
[                                      .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .   ]
Apodemus_flavicollis          ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Atherurus_macrourus           GTTA?GCTATGCGATCAGATTAGGTGTGGCAGGTGGTGGTAAGGACCAAGTATCTGGGAGAACCAGATGTGTCTCCCTCCTGAAGTGGAGTGGAGGTGATGATATGGGCCCACCCCTCTTCTCCCTGAGTGTATGCATTTGTCTTGCTTCATGAT--GGCTGATAAGACGGGTCTGGCCCCGTGTGGGGGTA-GCTCCTAATGAGGGCCTAAGCAGCAGGGCAAGGTGAGGTGGGGAAGAAGACCAGGGAGGGGAGAGAATGCATCAAGAGCCTGTCCCCGACTCCACTCTTTGAC----TAG
Cavia_porcellus               GTGAGGCTGTGCGGATCCATCGGGTGTGGCAGGCGGTGGTGAGGGTCAGGTATCAAGGAGAACCAGGTGTGTCTCTATCCTGAAGTGGAGTGGAGGTCTCGAGCTGGGCCC-TCCCTCTTCTCCCTGAGATTGTGCATTTTTCTTTCCTTATGATGGGGC---------GGGGCTGGCTC-GAATGGGGATGCCCTCCTGCTGAGAACCTAGGCAGCAGGGCCAGGGAAGGCAGGGAGGAAGACTGCAGGGCAGAGAG--TGTACTGAGAGCCTTCCCCTGCCTCCACCTCT-GAC----TAG
Cynomys_ludovicianus          GTGAGGCTGTGCGGGAATGCCAGGTGCGACAGGCAGAGGTGTGGGCCGGGCCTCTGGGGAGAACAACAGTGTCTCTCT-CTGAAACAGAGTGATGGTGGCCTGGTGGGCCCTTCCCTCTTGGCCATGAGCTTGTGCGTTTGCCTA-------------GCCAACAGGAGGGGGCTGGCTCTGT-TGGGGGGATCTTTGTGCTGAAGGCCTGAGCCACA-GGCAAGAAGAGGCAAGGGGCGAGACCAGGTCGTGGGCAGTG-------------TGCTCCTTACTCTACCCTTTGACTCACTAG
Glis_glis                     GTGAGACTGTGCGGGCAGGTCAGGTGTGGCAGGTAGAGGCATGGGCCAGCTCTCTGGGGAAAACAGCTGTGTTTCCCTCCTGAAGTGGAGTGAAGGCAG-AGCATGGGCTCTGCCCTCTTCCTC-------TGGGCCTTAGCCTTGCCTCGTGATGGGGCCCACAGGGCGGGGTCGGCCCTGTGCGGG-GGATCCTTCTGCTGAGGGTCTGAGCCACAGGGCAAGGCTAGGTGAGGAAAATGACCAGGGAGCGG-GAGTATGGGGCGAGGGCCTGCCCCTCACTCTACCCCCTGACTCACTAG
Homo_sapiens                  GTGAGGCCACACGGTCAGGGCAGGTGTGGCAGATGGAGCTGTAGGGCAAGTCTCCAGGGAGGACAGCTGTGTCTTCCCAATGAAGTGGAGTAGAGGTGGCCAGATGGACCTGTCCCTCTCCTCCCTGAGCCAGTGCATTTGCCTTGCCTGCTGATGGGGTCAACAGGACGCGGCTGGCCCTGTGTGGGGAAGTGCTCCTGCTGAGGGCCTGAGCAGCGGTGCAAGACTGGGGAAGAGGAAAGACTGGGTCTGGG----CATGTAGCGAGAGCCTGTAGTTGACTCCATCGTCTGACTCTCTAG
Hydrochoerus_hydrochaeris     GTAAGGCTGTGCGGATCCATCAGGTGTGGCAGGTGGTGGTGAGGACCAGGTATCAAGGAGAATCAGATGTATCTCTCTCCCGAAGTGGAGTGGAGGTCACAAGCTAGGCCCTTCCCTCTTCTCCCTGAGATTGTGCCTTTTTCTTTCCTTATGATGGAGCTGATGAGACGGGGCTGGCTCTGTATGGGGGTGCCCTCCTGCTGAGAACCTAAGCAGCAGGGCAAGGTAAGGCAGGGAGGAAGACTGCAGAGGGGAGAG--TATATTGAGAGCCTTCCCTTGCCTCCACCTCT-GAC----TAG
Microtus_duodecimcostatus     GTGAGTCTGTGCGCTCAGGTTAGGTATGGCAGGTAGAGGTATGGGCCAGGTGTCTTGGACACGCACTCGTGTCTTTTTTATGAAGTGATGTGGGGGTAGCCAGGTGACCCCTCTCCTCTTCTCCCTGAGTTCA----------CCACTTCACGATGGGACCGGCAGGCC----------------------------------------TGGGGTTCAGGGCAAGCTAGGCA--GAGAAAGGCTGGGAACGGAGAGCTGCAGAAGAGACACCGTGGTCTTGACTATCTGTTCTGCT-TGCTAG
Microtus_lusitanicus          GTGAGTCTGTGCGCTCAGGTTAGGTATGGCAGGTGGAGGTATGGGCCAGGTGTCTTGGACACGCACTCGTGTCTTTTTTATGAAGTGATGTGGGGGTAGCCAGGTGACCCCTCTCCTCTTCTCCCTGAGTTCA----------CCACTTCACGATGGGACCGGCAGGCC----------------------------------------TGGGGTTCAGGGCAAGCTAGGCA------------GAGAACGGAGAGCTGCAGAAGAGACACCGTGGTCTTGACTATCTTTTCTGCT-TGCTAG
Mus_musculus                  GTGAGGATGTGTGCTTAGGTTAGGTGTGGCA------GGTATGGGTCATGTTTCTTGGACAAGCAATTGTGTCTT----ATGAAGAGGTGTAGAGCTAACCAAATGGTCCCCCTCCCCAACCCTGCAAGTTCA----------TCACCTTATGATGGGGGCAGCAGACCGGGGCTGGGCCTGTGTGAGGGGGCCTTTCTGCTG-AGGCCTGAGCAGCAGGGCAAGCTAGGCAAGGAGAAGGGCTTGAAATGAAAAGGGTGTA----GGGAACACAATCCTGACTGTATATTCTGCCGTGTTAG
Myocastor_coypus              ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Octodontomys_gliroides        T---------GCAGTCAGGTCAGATATGGCAGGTGGTGGTGAGGACCAGATGTCATGAAGAACCAGAGGTGTCTCCCTCTGGAAGTGGAGTGGATGCGGTGAGGTGAGCCC----------TTCCTGAGTGCATGCGTTTGTCTTGCTTTATGATGGGGCTGATGAGACGGGGCTGGTCCTGTACGGGGACGCCCTCCTGCTGAGGGCCTAAGTGGTAGGGCAAGGTGAGGCAGGAGAGGGGA------------GAGTACATATCAAGAGCCTTCCCCTTCA-----CTGATGAC----TAG
Proechimys_guairae            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Rattus_norvegicus             GTGAGGGGGTGCGCTCGGGTTAGGTGTGGCAGGTACAGGTATGGGCCAGATTTCTTGGACAAGCAATTGGGTCTT----GTGAAGTGGTGTAGAGGTAACCAAACGGCCCC-CTCCCCAACTCTACAAGTTCA-----------CACCTCGTGATGGGGGCACCAGGTCGGGGCTGGCCCTGTGGGTGGGGGCCTTTCTGCTG-AGGCCTGAGCATCAGGGCAAGCTAGGAAAGGAGAAGGGCTTGAAGTGGAAGGGGTGTG----GGGGACACCATCTTGACGGTATATTCTGCTGTATTAG
Sciurus_vulgaris              GTGAGCCTGTGCGGGAATACCAGGTATGGAAGGTGGAGGTGTGGGCTGGGCCTCTGGGGGGAACAGCTGTATCTCCCT-CTGAAGTCAAGTGAAGGTGGCCTGGTGGGCCCTTCTCTCTTGGCCCTGAGCTCATGCATTTGCCTAGCCTCATGATGGGGCCAATAGGACGGGGCTGGCTCTGT-GGGGGGGATCCTTCTGCTG-AGGTCTGAGCTGCA-GGCAAGGAAAGACAA-GGGCAAGACCAGGTAGAGGACAGTATTCAGTGAGAGCCTGCTCCTTACTCCACCCTCTGACTCACTAG
;
END;