#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; 0:32 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:M19794]

	TITLE 'Mammal Nadsyn1-intron-4';
	LINK TAXA = Taxa;
	DIMENSIONS NCHAR=294;
	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          GTGGGGTGTCTGGCCTGTCGGGGATACCTTGTGGCACAGCACACGGAGGAGAATCAAGGTTGGGTTTGTTTGGGTTTTTTATCCTTGCCACCTGGACAATAGACAAGGTAAGGGAAGTCTGGCCACAGCCTCCAGCAAATTTGCATGATGGTGGATGGAGCCATGACCAAAACAGCTTAACCCTAGAGAAAGATTTCCCAGGGCTGCAGACTTGAAACAGCCCCAGAAAGTCTGCTCCTTTTCATAGAGAACTAAGTTTGGAGTTTGGTGTGAACAGTTTTTTCACCGCCATAG
Atherurus_macrourus           GTAAGCCGCTGGGCTTGCTGGAGGCCTTCTCGGGGACACCACACGAGAGAGACCCAGAGGAT{AG}GGGCCTGGGG---ATGCGTCCTTGTGGCCTTG----TGCTCTAGGTGAGGGAGCACTCTTTATAGCTGCCTGCAAAGCCACCCACCAGTGGGTGGAGCTGTGAGATGAAAAGCTGAAGCTCAGAGGAGATTTGCTCAGGGCTCTGTTCTTGAGCCTGCCTGGCATGGGTTATCTG---GCTTTGGTGATGATGATTGGAGCTTGGTGTGAGCAGCCCTGTTCCCGCTGCAG
Cavia_porcellus               GTAGGGCCCTGGGCTTGCCACAGCCCTTTTCAGGGACACCAAACGAGACACCCAGAGGGGGTGGGGCTTGGAG---GCGCGATCTTTCAGCCTGAATGTTAATCTAGGTGAGGGAGAACCCCTTTCAGCTGCCTGTGAGGTCACTTTTAGATGGATGGAGCTGTGAGAC--AAAGCTGAAGCTCAGAGGAGATTTATTCAGGGCTTGGTTCTTGAACCGACTC--CATGTATAACCTG---GCTTGGTTGGTGATGACTGCAGCTTGTCCTGACCTGCCCTGTTTCCGCTGTAG
Cynomys_ludovicianus          GTGGGGCTCTGGGCTTGCTGGAGACTCCCCTGGGGCCAATGCAC--------CCCAGAGGGAGGGCCCTGGGG-----CCCTGTGTGCTACCTGGACACTGGGCTAGGAGGGTG---TCTCCTCACCATGTCCAGCAGGGGCACCTGCCAGTGGGTGGGGCTGTCAGGGAC-------------------{AG}GATTTGTCTGGGCTGCAGTCTCGGGCTGGCTCTGCGTGGCGGTGCTCAGTCCTCTG-TGGCGGTGGCTAGAGCGCTGAGTGAGCCCCTTCCTGTCT----TAG
Glis_glis                     GTGGGGCCCTGGGCTCTCTGGAGGTGGCTTTAGATTCACATGACGGAGTGGCACCCGGGAGCGGGGCTTGGGG{AC}CATGCCCCTCTTG----------------CTAGATGAGGGCGGTCTCCTGGCAGCTGACAGCCGAGCCACCTGCGG-----TGTCGTCGTG-GGAGGGCAACTGAAGCCCAGAGATGATTTTCTCAGGGCTCCGTGCTTAGGCCGGCTCCGCGTGGTGTTACCA---------------------CGACCTCTGTGTGAGCGGCCCTGTTTCCTCTGCAG
Homo_sapiens                  GTAGGGCTCTCAGCTTGCTGGGAGGCTGCTTCTGGCCGATGCACGAGAGAGACGCAGAGGGTGGGGGTGTGGGGACACAGGTCCTTGTGGCCTGGAAGCCAGTCCAGGTGAGCAAGTTCCCTTGGAAGCTGCTGGGGAGGCCACCTTCTGATGGATGCAGCCATG--ATAGAAAGCGGAAGCCCAGAGAAGATTTGCTCGGGGCCCCATTCTCAAGCTGACTCTGCATGGCATCACCTCGTCACTTGGTGGCACTGACCGGAGCCCGGTGTGCACAGCCCTGTTCCCTCTGCAG
Hydrochoerus_hydrochaeris     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Microtus_duodecimcostatus     GTAAGGCGCCTGGCTGGTGGGGAATATCTTGAGGCACCGTACACGAAGGAGACCCAAGGTTGAGTTTGTTTGGGCTTTTTATCCTTGTCACCTGGACAATA---AAGGTGAGGGAAGTCTTCTGGCAGCTTCCAGCAAAGTCACTTGTTGGCCAGTGAAGTCATGAAGCAGAAAGCTTAAGCCTAGACAAGGCTTTCTCAGGGCCCTGGGCTTGAACCAGCTTCGGTGACCTCACCCTATCCTATGGGG---TAAGTTTGGAGGTTGGTATGATCAGTCCTTTTACCACTGTAG
Microtus_lusitanicus          GTAAGGCGCCTGGCTGGTGGGGAATATCTTGAGGCACCGTACACGAAGGAGACCCAAGGTTGAGTTTGTTTGGGCTTTTTATCCTTGTCACCTGGACAATA---AAGGTGAGGGAAGTCTTCTGGCAGCTTCCAGCAAAGTCATTTGTTGGCCAGTGAA{AG}TCATGAAGCAGAAAGCTTAAGCCTAGACAAGGCTTTCTCAGGGCCCTGGGCTTGAACCAGCTTCGGTGACCTCACCCTAT{CT}CTATGGGG---TAAGTTTGGAGGTTGGTATGATCAGTCCTTTTACCACTGTAG
Mus_musculus                  GTAGGGTGCCTGGCTTGTTGGGGATACCTTGAGGCACAGCATACGGAGGAGACTCAAGGTTGGGTTTGTTTGGGCTTTTTATCCTTGCCACCTGGACAATAGATAAGGTGGGGGAAGTCTCCTTGCAGGCTACAGCAAAGTCACATGTTGGTGGATAGAGCCATGAAACAGAAACCTTTAGCCTAGAGAAGGTTTGCTCAGGGCCCTGGTCTTGAGCCAGC-TCAGTAGCCTTATCTTATCCTATGGA----CAGATTTGAAGTGTGGTGTGAACAGTTTTTTCACCGCTGTAG
Myocastor_coypus              GTAGGGCCCTGGGCTTACCAGAGGTCTTCTCAGGGACACCACACGAGAAAGACCCAGTGAGTGGGGCTCGGGG---CCACGTCCTTGTGGCCCGAATGCTGCTCTAGGTGAGGGAGAAAGCCTTATAGCTGCCTGCAGGGTCACCTGTTGGTGGGTGGAGCTGTGAGACAAAAAGCCGAAGCTCAGAGGAGATTTTCTCAGGGCTCAGTTCTTGAGCCAGCTGTGCATGTGTGATCTG---GCTTGGGTGGTGGTGACTGGGGCTTGATATGAGCATCCCTGTTCCCGCTGCAG
Octodontomys_gliroides        GTAGGGCTGTGGGCTTGCCAGAGGTATTCTTGGGGACACCACACGAGAAAGGCCCAA-GGGTGGGGCTTAGGG---TCACATCCTTGTGACCTGAATGCTATTCTAGCTAAGGGAGAAATCCTTACAGCTGCCTATAAGGTAAACTGCCGGTACATGGAGCTGTGAGACAGAAAGCTAAAGCTCAGAGGAGATTTGCTCATGGCGCAGTTCTTGAGCCAACTCTGCATG-----------------GGTGGTGGTGACTGGAGCTTGTTGTGAGCATCCCTGTTCCCGCTGCAG
Proechimys_guairae            GTAGGGCGCTGGGCTTACCAGAGGTCTCCTCAGGGATACCACATGAGAAAGACCCAGGAGGTAGGGCTTGGGG---CAACGTCCTTGTGGCCTGAATGCTGCTCTAGGTGAGGGAGAAATCCTGACAGCTGCCTGCAGGGTCACTCGTTGGCGGGTGGAGCTGTGAGACAAAAAGCTGAAGCTCAGAGGATTCTTGCTCAGGGCCCGGTTCTTTAGCCAGCTGTGGGCGCGTTGTCTG---TCTTGGGTGGTGGTGACTGGGGCTTGATGTGAGCGTCCCTGTTCCCGTTACAG
Rattus_norvegicus             GTAGGGTGCCTGGCCTGTCGGGGAGACCTTGTG-----GCACACGGAGGAGACTCAAGGTTGGGTTTCTTTGGGTTTCTTATCCTTGCTACCTGGACAATAGACAAGGTGAGGGAAGCTTCCTTGCAGCCTACAGCAAAGTCATGTGCTGGTGGATGGAACCATGAAACAGAAAACTTAAGCCTAGAGAAGGTTTGGTCAGAGCCCTAGTCTTGAACCAGC-TCAGTAGCCTTACCATATCCTAT-GGA---CAGATTGGGAGTTTGGTGTGAACAGTTTTTTCACTGCCATAG
Sciurus_vulgaris              GTGGGGCTCTGGGCTTGCTGGAGGTGC------GGCCGATACAC--------CCCAGAGGGTGGGGCCTGGGG-------CCCTGCGTTGCCTAGACAGTGGCCTAGGTGGGAG--GTCTCCCCGCTGCTGCCAGCAGGG-CGCCAGCTGGTGGATGGGGCTGTCAGGGATGG-----------------GATTTGTTTGGGGCTGCATTCCCAGGCTGGCCCC{GT}CATGGTGCTGCCTAGCCCTCTGGTGGCAGTGACTGGAGCCCTGTGTGAGCAGCCCTGTTCCTTCCACAG
;
END;