#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; 21:23 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:M19789]

	TITLE 'Mammal Abcb9-intron-2';
	LINK TAXA = Taxa;
	DIMENSIONS NCHAR=280;
	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]
[                                      .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .]
Apodemus_flavicollis          GTAGCCACCCAACGGCAGGAGGGTGCAGGAGCAGCCCAGCACCGCAGCAAC--CCCACACTGACTCGGAA-------CCCTTTGCTTGGGCCACAGCCTGGAGCCATGCCCTCTTGTCTCTGAAAATGGCTCCAGTCCCTGGTTGGTTGCCAGTGTTGAGTCCTTACCCTCTTACTGGGGGAGTGAGGAGGTCCCCTACAGAGGG--AGAAGGGGCTGCTGGTGGGCGGCGCTGCCTGCCGGAAGGATGCCG-GCTATACCGTCTCTCATCTGCAATCAG
Atherurus_macrourus           GTAGCCACTCCGCGGGGGCCCTGTCCCTCAGCCCGTCACTGCAGTGACCAGCTCCCAAGCCAGCTAGGAGCCCATGTCTCTGAGGAGGGCCGTACCCTAGGAGACATACCCGCTGCTCTCTGAAAGTGGCGTTGGTCCCTGGCTGGTTGACAGCTTTGGGTCCCTTGTCCCTGGCTGGGGAATGCGGGGGACCCCCTGAAGAGTGGCGGAGGGGCGGCCGGGTGGTGGCTGTCGCTTGTCGGAAGGACGTCGTGCTATAACATCTTTTATCTGCAATTAG
Cavia_porcellus               GTAGCCGCCC-GCGGGGGCCCTGTCCCTCGGCCCGTCACCTCAGTGACCGGT-CCTGAGCCAGCCTAGCACCTCATCCCTGCAGCAGGCAGGCCAC-------------------GTCCTAAATCGAGGCTTCAGCCCCTGGCTGGTTGGCAGCTCTGGGTCCCCTGTCC--------------GGAGGGGCCCCTGGCAGTGGGAGGGGAGGGCGGGCGGGTGGTGGCTGCCGCTCCTCGGA--GGCCGCGCGCTATAACATCTGTTATCTGCAATTAG
Cynomys_ludovicianus          GTAGCCACTCGGCG--GGACCTGTCCGACAGCC---------CGTGACCAGCTCCCAAACTGGCTTAGAAACCTCGTCCCTGTGATCAGACCACATCCTAGTGCTGCACCCTCTTGTC-------------TTGGTCCCTTGCTGCTTGGCAGAGCTGGGCCCCTTGCCTCCCACAGGGAAAGAGGGACACCCCCCTGGACAGTGGCGGAGGGGCGGCCGGGTGGTGGTTGTCGCA-GTCGGAAGGACGCGGTGCTATAACATCTCTTATCTGCAATTAG
Glis_glis                     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Homo_sapiens                  GTAGCTGGCTCAAGGTGGGCCTGTCCCTCAGCTGGTCACCCTGGGAACCGGCTTCCACACTGTCTTAGA-----------------------GCACCCTAGAACCACACCCTCTGGTCCCTGAAAAGGGCTTCAGTCCCTGGCTGTTTGGCACATTTGGGTCTCTTGTCCCCCACTGGGAATGAGGGGGACCCCCCTGGAGTGGGGCGGAGGGGGCAGCCGGGTGTGGTCACTGGT--CTGGAAGGACATCGTGCTATAATATCTCTTATCTGCAATTAG
Hydrochoerus_hydrochaeris     GTAGCGGCCCTGCGGGGGCCCTGTCCCTCAGCCCGTCACCCCAGTGACCGGTCCCCGAGCCAGCCTAGTGCCTCGTCCCTGCAGCAGGCAGGCCAC-------------------GTCCTAGATCGAGCCTTCAGCCCCCAGCTGGCTGTCAGCTCCGGGTCCCCTGTCCCTGGCTGCAGACCGAGAGGAGCCCCCGGCAGC-----GGGAGGGCGGCCGGGTGGTGGCTGCCGCTCCCCGGA--GGCCGC-CGCTATAACGTCTCTTATCTGCAATTAG
Microtus_duodecimcostatus     GTAGCCACCCAACGGCAGCAGGGTGCAGGAGCAGCTCAGCACCATGGCTGCGTCCCAGAGTAGCTTTGAA-------CCCTTTGGTTGGGCCACACCTAAAAGCCACACTCTCTTGTCTCTGAAGATGGCACCAGTCCCTGGCTGGTTGACAGTGTTGAGTCCCTCACCCCTTACTGGGGAAT-GAGAGGGTCCCCTACAGAGTGGCGGGAGGGTCAGTGGGTGGTGGCTGCTGCCTGCCGGAAGGACACC--GCTATACCGTCTCTCATCTGCAATCAG
Microtus_lusitanicus          GTAGCCACCCAACGGCAGCAGGGTGCAGGAGCAGCTCAGCACCATGGCTGCGTCCCAGAGTAGCTTTGAA-------CCCTTTGGTTGGGCCACACCTAAAAGCCACACTCTCTTGTCTCTGAAGATGGCACCAGTCCCTGGCTGGTTGACAGTGTTGAGTCCCTCACCCCTTACTGGGGAAT-GAGGGGGTCCCCTACAGAGTGGCGGGAGGGTCAGTGGGTGGTGGCTGCTGCCTGCCGGAAGGACACC--GCTATACCGTCTCTCATCTGCAATCAG
Mus_musculus                  GTAGCCACCCAACGGCAGAAGGGAGCAGGGCCAGCCCAGCACTGCAGCAACCGCCCAGACTGACGTGGAA-------CCCTTTGGTTGGGCCACATCCCAGAGCTGTACCCTCTTGCCTCTGAAGATGGCTCCAGTCCCTGGCTGGTTGCCAGTGTTAAGTCCTTTACCCCTTACTGGGGAG--TGAGGGGTCCCCTACAGAGTGGCAGGAGGGGCTGCTGGTGGGTGATGCTGCCTGCCGGAAGGACACCG-GCTATACCGTCTCTCATCTTCAATCAG
Myocastor_coypus              GTAGCG-CCACACTGGGGCCCTGTCCCTCTGCCCATCACCATGGTGACCAGAGCCTGAGCCGGCATAGGACCCCTACCCCTGAGGTGGAGGCATCT----------------------CCTCAAATTGGCTTCAGCCC-------------------GGGTCTCTTGCCCC-GGCTGCAGAATGAAGGGACCACCCTGGAGTGTGCCGGAGGGGGAGCCGGGTGGTGGTTGCCGCTGGTCGGATGGACGTCGTGCTATAACATCTCTTATCTGCAATTAG
Octodontomys_gliroides        GTAGCACCCGCG-CGGGGCCCCTTCCCTCTGCCC-CTGCCACGGTGACTAGAGCCTGAGCCGGTGTAGGACCCCTGTCCGTGAGGTGGAGGCATCT-----------------------CCTAAATGGGCTTTGGCCC-------------------GGGTCTCCTGTCCC-GACTGCAGAATGAAGGGACCCCCATGCAGAGTGCCGGAGGAGAGGCCGGGTGGTGGCTGCCGCTGGTCGGAAGGACACGGTGCTATAACATCTCTTATCTGCAATTAG
Proechimys_guairae            GTAGCGCCCACACCGGGGCCCTGTCCCTCTGCCCATCACCATGGTGACCAGAGCCCGAGCCAGCATGGGACCCCTACCCCTGAGGTGGAGGCGTCT----------------------CCTCAAATTGGCTTCAGCCC-------------------GGGTCTCCTGTCCCGGGCTACAGAATGAAAGGACCGCCCTGGAGGGTGTCAGAGGGGAGGCCGGGTGGTGGCTGCCGCTTGTCGGAAGGACGTCGTGCTATAACATCTCTTATCTGCAATTAG
Rattus_norvegicus             GTAGCCACCCAACGGCAGGAGGGTGCAGGACCGGCCCAGCACCGCGGCAACCTCCCAAACTGACTTGGAA-------CCCTTTGGTTGGGCCACATCCTAGAGCCATACCCTCTTGACTCTGAAAATGGCTC------CTGGCTGTTTGACAGTGTTGAGTCCCTTACCC--------------TGGGGAGTCCCCTACAGAGTGGCGAAGGGGGCTGTTGGTGGGTGGCGCTGCCTGCCGGAAGGACACCG-GCTATACCGTCTCTCATCTGCAATCAG
Sciurus_vulgaris              GTAGCCACCTGACG--GGGCCTGTCCATCAGCC-GCCGCCATGGTGACCAGCTCCCAAACTGGCTTAGAACCCACGTCCCTTTGAT-AGGCCACCCTCTAGAGCTGCGCCCTCTGGTC-------------TCAGTCCCCGGCTGTGTGGCAGATCTGGGTCCCTTGCCCCCCACAGGAAATGAGGGAGACCCCCCTGGAGAGTGGCGGTGGGGGCGGCGGGTGGTGGCTGTCGCT-GCCGGAAGGACGCGGTGCTATAACATCTCTTATCTGCAATTAG
;
END;