#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:M19795]

	TITLE 'Mammal Rras-intron-4';
	LINK TAXA = Taxa;
	DIMENSIONS NCHAR=421;
	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       310       320       330       340       350       360       370       380       390       400       410       420    ]
[                                      .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .    ]
Apodemus_flavicollis          GTTTGGGTGCCACCTCCCCTGATAACATTTGGCCCTACCAAGCGCTCTCGGGACCATCTCCTACTGGATCCCTGGTCTCTCTACTGTCACATCTTCCACTTAGATG---ACCCCCCAAGTGGAATAACCCATCGCTTAGCCACACTCCATCATTGAGGGATTCTAGGCAGGACCTCTAGAA------------------------CCTGGTCCCTACTTATAGCATATGCTCCCTGTC--------------------CCTGCCCCAGTTAACATCTTCATAATCTCCTGACATCTCACT--GAGGTAGCTTCGACCCTCCAGGACCCTCCTCTTGGGTCTTTCTAGAACTTTCTCTCCTGAGCCTGCTGAGCTT----GCGGCTTTCAGTGTCCCCTCTCCCTGACCTTTCCCTCTGTCT
Atherurus_macrourus           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Cavia_porcellus               GTATGGGTGCCTCCTTCTGATGTACCATCAGCACCCC----GCCTGCCCAGGAGCCCCCACTTCTGTGCCCTTTCTTCTGTGCTTGTCACTTCCTGGACATAAAGATGTGATTTCCACACAGAACT---CATCTTTTAGCCGAAT--CTTCTTTGGGGATTTCCAGCT-------------CTACACTTGGCCTCTGCCAAGACCAACA-TCCTTACTTGTAGCCTGCAGACTCTGTCTTAAATAAAAACCCTGGCTTCCATCCCAAACTAGCCTCCTGAGCTGGTCCTGATTCCTTATTTCTATGATGTTAACACTCCC--------------AGCATCCCATAGGAACTTTCCCTCTGGAGCTCCCAGGGCCTTTTGGCTTCCCTAGCTGGGGTCACTCCCTGACTCCTCTCCCCTGCA
Cynomys_ludovicianus          GTTTGGGTGCCGCCTTCCCTGGGGACAAATGGGTTTGGGAGGCTCCGTCCAGAGCATCCTCCTCTGCATCTCTGCTCCCTCCCATGCCACGCTTCTCATTTGGCTGTGTTATTCCCAAGTGGGACCATCCATTATTCACCAGAGGGCCCCCAGGACAGATGGATGGATGGGGCAAAGGGCACTGCCCCTTGCCCCCTCTTTTCCCACCTAGCTCTCCCCACAGTCTCTCCTTCCTCTACCACTGAAACACCCCCAACCCACACCCTAGTTAACGTCCATGAAACCTCCCGA{CT}TCCTCACTTGAATGGCACCTACTCCCTC---AACATCCACCCGGGATCTTTCTGCAACTTTCCCCTT-GAGCCACCAAAG-------GCTTCCCCAGCTGGGGTCACCCCCTGATTCGTGTCCATAACC
Glis_glis                     -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Homo_sapiens                  GTTCGGGCACCCCTCTTTCTGGGGACATCTCAGTCTGGGAGGCTCCTTCCAGAGCATCCTCCTCTGCAGTGCTGCGACTGCCACTGTCACACAGCTCACCTAGATGGGTTACCCCCAAACTGGACCTTCCATCACCGAGCAGAGGGCCCTCAGGAGAGGCTGCTGGACGGAACAAAGGACACAGCTCTCTTTGCCCCTTCCTCGCATTCCTCCCTTCCAGCCAACCTCCCACCCTGCCTCTGCCGAACACCCTGACTTCCCTGCCTGGTTAGTGCCCACGAAGCCCCCCCATCCCTTACTTAGAAGACACCAAGCCCCTGCGGCATCTCCCTCCATAATCTCTCAGGAGCTCTTCCTCTTGAGTTCTCACAGCCTGTCTGTCTCTCTGGCTGCGGTCACCCCCTGACTCCCCCGTGTCCCC
Hydrochoerus_hydrochaeris     GTATGGGTGCCCCCCTTCCGAGGTACATCAGCACCCCGCCTGCCTGCCCAGGAGCCCCTACTCCTTTGTGTTCTCTTCTGCACTTGTCACTTCCTGGACACAAAGGTGTGATTTCCACATAGAACT---CATCTTTTAGCTGAAT--CTCCTTTGGGCATTTCCAGCC-------------CTATACTTGGCCTGTGCCAAGACCGACAATCCTCACTTGTAGCCTGCAGACTCTGTCTTAAACAAAAACCTTGGGTTCCATCCCAACCTAGTCTCCTGAGCTGGTCCTGATTCCTTATTCATA---TGTCAAAACTCCC--------------TGCATCCCACAGGAACTTTCCCTCTGGAGCTCCCAGTGCCTGTTGGCTTCCCTAGCTGGGGTCACTCCCTGATTCCTCTCCCCTGCC
Microtus_duodecimcostatus     GTTTGGGTGCCCCCTTCCTTGATGGCATTTGGACCTAGGAGGCTCTCTCGGGAACCTCTCCTTCCTGGTCCCTGGTCCCTTCACTGTCAGAACTTTCACTTCGACG---AACCCACAAATGGAACCATCTATCACTGAGCCACACCCCCTCACTAGGGGATTCTAGGCAGGGGTTCCATCACTGACCATCACATAATCCTTTGCTCCTGCACCCTAGCTGCAGTGTGTGTTCCCTCTCGTAGCTAAGCACCCT-----------------AACTTCTTCCCTGCCTCCTGAAGTCTCACTTAGATATAGTTTCAACTCTCCAGTATCCTCCTGTTGGGTCT----------TTCTTTCTTGAGCCTGCTCAGCCTT------GCTTCTGTCAGCCCCCCACCCCAACTCCTTGCTTTGTCC
Microtus_lusitanicus          GTTTGGGTGCCCCCTTCCTTGATGGCATTTGGACCTAGGAGGCTCTCTCGGGAACCTCTCCTTCCTGGTCCCTGGTCCCTTCACTGTCAGAACTTTCACTTCGACG---AACCCACAAATGGAACCATCTATCACTGAGCCACACCCCCTCACTAGGGGATTCTAGGCAGGGGTTCCATCACTGACCATCACATAATCCTTTGCTCCTGCACCCTAGCTGCAGTGTGTGTTCCCTCTC{CG}TAGCTAAGCACCCT-----------------AACTTCTTCCCTGCCTCCTGAAGTCTCACTTAGATATAGTTTCAACTCTCCAGTATCCTCCTGTTGGGTCT----------TTCTTTCTTGAGCCTGCTCAGCCTT------GCTTCTGTCAGCCCCCCACCCCAACTCCTTGCTTTGTCC
Mus_musculus                  GTTTGAGTGCCCCCTCCCCTGGTCACATTTGGACCTAGGAAGCTCTCTCAGGACCATCTCCTACTGGATCCCTGGTCCCTCTATTGTCACAACTTTCACTTAGATG---ACCCCCCAAGAGGAATCGCCCATCACTGAGCCACACCCCATCACTGAGGGATTCTAACCAGGACCCCTAGCATGGCCCTTATACTAATCCGTTGATACTG-------------------GTTCCCTGTCCTGAACAAACACCCTTACTTCTTGCCCCAGTTAACACCTTCATAATCTCCTGACATCTCACT--GATATCACTTCAACCCTCCAGTAGCCTCCTCTGGGGTCTTTCTAGAACTTTCTATCTTGAGCCTGCTGCACCTTGCGGCGGCTTTCAGCATCTCCTCTCTCCGACGCCTCCCTTTGTCC
Myocastor_coypus              -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Octodontomys_gliroides        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Proechimys_guairae            -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Rattus_norvegicus             GTTTGGGTGCCCCCTCCCCTGATCACATTAGGACCCAGGAAGCTCTCTCAGGACTGTCTCCTACTGGATCACTGGTCTCTCTACTGTCACAACTTTGACTTATATG---ACCCCCCAAGTAG-ATCACCCATTGCTGAGCCACACCCCATCACTGAGGGATTCTAGGCAGGACCCC-AGCACAGCCCTTCTAGTAATCCTTGGATACTGGTCCCTACTTGTAGTATATGTTCCCTCTCCTGAACAGACACCCTTACTTCTTGCCCTAGTTAACATCTTCATAATCTCCCGACATCTCGCG-----------TGTATCCTCCAGGATCCTCCTCTTGGGTCCTTCTAGAACTTTCTATCTTGAGGCTGATGAGCCTT---ACGGCTTTTGGCATCTCCTCTCTCTGACCCCTCCCTCTGACC
Sciurus_vulgaris              GTTTGGGTGCTGCCTTCCCTGG------------------GGCTCCGTCTGGAGCATCCTCCTTTGCATCCCTGCCCCCTCCAATGCCACACTCCTCACTTGGATGTGTTATCCCCAAGTTGGACCATCCCTCATTCACCAGAGGGCCCCCAC------------GATGGGGCAAGGGGCACTGCCCTGTCTTCCTGCTTTCCCACCTAGCCTCTCCTCACAGTCTTCCCGTCCTCTACCACTGAAACACCCCCAACCCACACCCTAGTTAACG--------AACCCCTGATTCCTCACTTGAATGGTATCAACTCCCTC---AGCATCCACCCAGGATCTTTCTGGAACTTTCCCCTT-GAGCCACCACAGCCTGTCTGCCTCCCCAGCTGGGGC--CCCCCTGATTCCTGTGTCTTCAC
;
END;