#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 April 26, 2024; 3:22 GMT

TreeBASE (cc) 1994-2008

Study reference:
Farwick A., Jordan U., Fuellen G., Huchon D., Catzeflis F., Brosius J., & Schmitz
J. 2006. Automated Scanning for Phylogenetically Informative Transposed Elements
in Rodents. Systematic Biology, 55(6): 936-948.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S1619]

BEGIN TAXA;
        TITLE  Taxa1;
        DIMENSIONS NTAX=23;
        TAXLABELS
            Anomalurus_sp
            Castor_fiber
            Cavia_porcellus
            Coendou_prehensilis
            Cricetus_cricetus
            Ctenodactylus_gundi
            Dolichotis_patagonum
            Glis_glis
            Heteromys_gaumeri
            Jaculus_jaculus
            Marmota_Marmota
            Meriones_unguiculatus
            Mus_musculus
            Myocastor_coypus
            Nannospalax_ehrenbergi
            Octodon_degus
            Ondatra_zibethicus
            Oryctolagus_cuniculus
            Pedetes_capensis
            Proechimys_cuvieri
            Rattus_norvegicus
            Sciurus_vulgaris
            Thryonomys_swinderianus
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2575]

	TITLE 'SINE presence-absence';
	LINK TAXA = Taxa1;
	DIMENSIONS NCHAR=31;
	FORMAT DATATYPE=Standard SYMBOLS= "0 1" MISSING=? GAP= -;
	CHARSTATELABELS
		1  char1,
		2  char2,
		3  char3,
		4  char4,
		5  char5,
		6  char6,
		7  char7,
		8  char8,
		9  char9,
		10  char10,
		11  char11,
		12  char12,
		13  char13,
		14  char14,
		15  char15,
		16  char16,
		17  char17,
		18  char18,
		19  char19,
		20  char20,
		21  char21,
		22  char22,
		23  char23,
		24  char24,
		25  char25,
		26  char26,
		27  char27,
		28  char28,
		29  char29,
		30  char30,
		31  char31,
		;

MATRIX
[                                   10        20        30 ]
[                                    .         .         . ]
Anomalurus_sp               ?00000000?0000?000011100000?100
Castor_fiber                ?????0???00???00000100000??????
Cavia_porcellus             000000001?000000000000111001111
Coendou_prehensilis         ?0000??01??????0000000110000100
Cricetus_cricetus           0000011101110011111100000??0100
Ctenodactylus_gundi         ?00000???0?????0??00001000001??
Dolichotis_patagonum        ?00000001??000?0??0000111001111
Glis_glis                   ?????00????0000???0000000??0???
Heteromys_gaumeri           ?0000?0??0????????0100000??????
Jaculus_jaculus             00000?000??00001101100000000???
Marmota_Marmota             ??????0????011?0??0????????0100
Meriones_unguiculatus       11??011101?10011101100000000???
Mus_musculus                1100011101110011101100000000100
Myocastor_coypus            ?011100????????0000000110110100
Nannospalax_ehrenbergi      ?????00000000011101100000000100
Octodon_degus               ?0111???????????00?00011000?100
Ondatra_zibethicus          000001110111001111?10000000????
Oryctolagus_cuniculus       000000?00?0000?0000000000000000
Pedetes_capensis            0000000????00000000111000000???
Proechimys_cuvieri          001110001??????000?000110110100
Rattus_norvegicus           1100011101?10011101100000000100
Sciurus_vulgaris            ?0000?0??0?01100000000000000100
Thryonomys_swinderianus     ?00000000??000????00001?0??0100
;
END;

BEGIN TREES;
      TITLE Tb7940;
      LINK TAXA = Taxa1;
         TRANSLATE
            1    Dolichotis_patagonum,
            2    Cavia_porcellus,
            3    Octodon_degus,
            4    Myocastor_coypus,
            5    Proechimys_cuvieri,
            6    Thryonomys_swinderianus,
            7    Ctenodactylus_gundi,
            8    Heteromys_gaumeri,
            9    Castor_fiber,
            10   Anomalurus_sp,
            11   Pedetes_capensis,
            12   Jaculus_jaculus,
            13   Nannospalax_ehrenbergi,
            14   Ondatra_zibethicus,
            15   Oryctolagus_cuniculus,
            16   Glis_glis,
            17   Marmota_Marmota,
            18   Cricetus_cricetus,
            19   Meriones_unguiculatus,
            20   Rattus_norvegicus,
            21   Mus_musculus,
            22   Sciurus_vulgaris,
            23   Coendou_prehensilis;
      TREE 'Fig. S-1' = [&R] ((((((21,20,19),(18,14)),13),12),(11,10),9,8),(7,6,(((5,4),3),(2,1),23)),(22,17),16,15);



END;