#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 July 09, 2025; 13:35 GMT

TreeBASE (cc) 1994-2008

Study reference:
Page R., Lee P., Becher S., Griffiths R., & Clayton D. 1998. A different tempo of
mitochondrial DNA evolution in birds and their parasitic lice. Molecular Phylogenetics
and Evolution, 9(2): 276-293.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S423]

BEGIN TAXA;
        TITLE  maximum_likelihood;
        DIMENSIONS NTAX=20;
        TAXLABELS
            Dennyus_adamsae_U96427
            Dennyus_adamsae_U96428
            Dennyus_carljonesi_carljonesi
            Dennyus_carljonesi_forresteri
            Dennyus_carljonesi_fosteri
            Dennyus_collinsi
            Dennyus_cypsiurus
            Dennyus_distinctus_distinctus
            Dennyus_distinctus_timjonesi_1
            Dennyus_distinctus_timjonesi_2
            Dennyus_hirundinis
            Dennyus_simberloffi
            Dennyus_singhi
            Dennyus_somadikartai__U96418
            Dennyus_somadikartai_U96419
            Dennyus_thompsoni_U96424
            Dennyus_thompsoni_U96425
            Dennyus_vauxi
            Dennyus_wellsi
            Dennyus_wraggi
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2145]

	TITLE Fig._4;
	LINK TAXA = maximum_likelihood;
	DIMENSIONS NCHAR=505;
	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       430       440       450       460       470       480       490       500       510       520   ]
[                                           .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .   ]
Dennyus_adamsae_U96427             TAAATCCTATCTTTTTACTCCAATAACCTGACTATCTGGGGTCAGGTTATACCTTGCGTTTATAGCAGCTGCTTTCCTAGGTTATGTTCTACCCTGAGGACAAATATCTTATTGAGGGGCCACTGTTATTACTAACCTAATTAGAGCTGTTCCATATTTAGGTAACTCACTAGTAGAATGAATCTGAGGAGGTTTTAGTGTCGGTAGGCCAACTCTAACCCGATTTTTTACACTACATTATATTACGCCTCTTTTAGGAAGGTGTTTAGTTATAATTCATTTATTTTTTTTACATGAAACGGGAAGAAGAAATCCTCTTGGTTTAGGAAAAAACAGGGATAAGATTTTTTTCCATCCTTTTTTTTCCTTTAAAGATTTAATTGGTTTTTTTTTTTTTTTTTTATTTATTTTTTTTTTTTGTTTGAAATTTCCTATCGTGTTTCTGGATTCTGACAATTTTTTAATTGCAAATCCTATAGTCACACCTGTTCACATTCAACCTGAA
Dennyus_adamsae_U96428             TAAATCCTATCTTTTTACTCCAATAACCTGACTATCTGGGGTCAGGTTATACCTTGCGTTTATAGCAGCTGCTTTCCTAGGTTATGTTCTACCATGAGGACAAATATCTTATTGAGGGGCCACTGTTATTACTAACCTAATTAGAGCTGTTCCATATTTAGGTAACTCACTAGTAGAATGAATCTGAGGAGGTTTTAGTGTCGGTAGGCCAACTCTAACCCGATTTTTTACACTACATTATATTACGCCTCTTTTAGGAAGGTGTTTAGTTATAATTCATTTATTTTTTTTACATGAAACGGGAAGAAGAAATCCTCTTGGTTTAGGAAAAAACAGGGATAAGATTTTTTTCCATCCTTTTTTTTCCTTTAAAGATTTAATTGGTTTTTTTTTTTTTTTTT{AT}{AT}TT{AT}{AT}TTTTTTTTTTTTTTTT{AG}A????????????????????????????????????????????????????????????????????????????????
Dennyus_carljonesi_carljonesi      TAAATCTTATTTAAATTCCCCTTTTACCTGAGCATCAGGTATTTTTATTTTTTTTTTATTTATAGCATCAGCTTTTTTAGGCTACGTTTTACCTTGAGGTCAAATGTCATATTGAGGGGCAACCGTGATTACAAATTTAATTAGCGCCCTACCTTATTTAGGAAGTTTTTTAGTAGAGTGAATTTGAGGAGGTTTTTCGGTTGGAAATCCAACTTTAACACGTTTTTTTTCTCTCCACTATCTAACTCCCTTACTTTCTTCTTTTTTTGTTTTTTTTCATTTATTTT?TTTACATGAAACAGGAAGAAGAAATCCTCTTGGACTTGGAAAAAACAGGGATAAAGTTTTTTTTCATCCTTATTTTACTATAAAAGATTATATTGGTTTTGTTCTTTTTTTTTTTTTTATTTCTATTTCTAGGCAAAAATCC???????????????????????????????????????????????????????????????????????????
Dennyus_carljonesi_forresteri      TAAATCTTATTTAAATTCTCCTTTTACATGAGTGTCAGGTGTATTTATTTTTTTTTTATTTATAGCAGCAGCTTTTTTAGGTTATGTTTTACCTTGAGGTCAAATATCATACTGAGGGGCGACTGTAATCACTAATTTAATTAGTGCTGTACCTTATTTAGGAGGTTTTCTAGTAGAATGAATTTGAGGAGGTTTTTCAGTTGGTAATCCAACTTTAACACGTTTTTTTTCGTTTCACTATTTAACTCCTCTCCTCTCCTCTTTTTTTATTTTTTTTCATTTATTTTTTCTACATGAAACAGGAAGAAGAAATCCTCTTGGGCTTGGCAAAAATAGAGATAAGGTTTATTTTCATCCTTATTTTACTATAAAGGATTTTCTTGGTTTTCTTTTTTTTGTTTATTTTTTATTTATTTTTAGATTAAAATTCCCTACTTTTTTTATAGATTCAGATAATTGAATAATTGCAAATCCAATAACTACCCCAATCCATATTCAACCTGAA
Dennyus_carljonesi_fosteri         TAAATCTTATTTAAATTCTCCTTTTACATGAGTGTCAGGTGTATTTATTTTTGTTATATTTATAGCAGCAGCTTTTTTAGGTTATGTTTTACCTTGAGGTCAAATATCATACTGAGGGGCGACTGTAATCACTAATTTAATTAGTGCTTTACCTTATCTAGGAGGTTTTCTAGTAGAATGAATTTGAGGGGGTTTTTCAGTTGGAAATCCAACTTTAACACGTTTTTTTTCGTTTCACTATTTAACTCCTCTTCTCTCTTTATTTTTTATTTTTTTTCATTTATTTTATTTACATGAAACAGGAAGAAGAAATCCTCTTGGACTTGGCAAAAATAGGGATAAGGTTTATTTTCATCCTTACTTTACTTTAAAGGATTATCTTGGATTTATTTTTTTTATTTATTTTTTATTTATTTTTAGATTAAAATTCCCTACTTTTTTTATAGATTCAGATAATTGAATAATTGCAAATCCAATAACTACTCCAATCCATATTCAACCTGAA
Dennyus_collinsi                   TAAATCCTACCTTTTTACCCCAATAACCTGACTATCTGGAGTAAGACTATACCTGGCATTTATAGCAGCTGCTTTCCTAGGTTATGTTCTACCTTGAGGACAAATATCTTATTGAGGAGCTACTGTTATTACTAATCTTATTAGAGCAGTCCCATACTTAGGCAACTCATTAGTAGAATGAGTCTGAGGAGGTTTTAGTGTTGG?AGCCCAA{AC}CTTAACCCGATTTTTCACACTGCACTATATTACGCCTCTTTTAGGAAGATGTTTAGTTATAATTCATTTATTTTTTTTACATGAAACAGGAAGAAGGAATCCTCTTGGTCTAGGAAAAAACAGAGATAAGATTTTTTTCCATCCTTTTTTTTCCTTTAAAGATTTAATTGGTTTTTTATTTTTTTTTTTATCCATCTTATTTTTTTGTTTAAAATTTCCTGTTGTGTTCCTGGATTCTGACAATTTTTTAATGGCTAATCCTATAGGTACGCCAGTTCACATTCAACCTGAA
Dennyus_cypsiurus                  ???GTCCTATTTAAATCTTTCCCTAACCTGAATGAGAGGTTTAACTCTCTACTTATTATTTATAGGGGTAGCTTTTTTAGGCTACGTTTTACCTTGGGGCCAAATATCATTTTGAGGGGCTACAGTAATTACTAATTTAATTAGTGCTATTCCTTATTTTGGAAGTTCACTAGTTGAATGAATTTGAGGGGGGTTCTCAGTAAGAAATCCTACTTTGACTCGATTTTTCACATTACACTACTCTATGCCTATTATTAGGATAAGACTAATTTTTAGGCATTTAATTTTTTTACATGAAACAGGAAGATCTAATCCGCTTGGATTAGGAAAAAATAGAGATAAAATTTTTTTTCATCCTTTTTTTACATTAAAAGATGTATTAGGATTTATTTTATTTAGTTTTATTTTATTTTTCTTCAGAATAAAATTGCCAAACTTTTTTTTAGATACTGACAACTTTATTCTTGCTAATCCATTAGTCACTCCTGTTCATATTCAGCCTGAG
Dennyus_distinctus_distinctus      TAAGTCTTATTTAAATTCACCTTTTACTTGAGTATCAGGTGTTATTATTTTTTTCTTATTTATAGCAGCAGCTTTCTTAGGTTATGTCTTGCCTTGAGGTCAAATATCTTATTGAGGAGCAACTGTAATTACTAATTTAATTAGAGCCTTGCCTTACTTAGGAACTTTTTTAGTTGAGTGAGTTTGAGGAGGTTTTTCAGTTGGCAATCCAACTTTAACACGTTTTTTTTCTTTTCATTACCTAACTCCTTTACTTTCTTCTCTTTTTGTTTTTTTTCATTTATTTTTTTTACATGAAACAGGAAGAAGAAATCCCCTTGGACTTGGAAAAAATAGAGATAAAGTTTTTTTCCATCCTTTTTTTTCTTATAAAGACGTTCTTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTAAA???????????????????????????????????????????????????????????????????????????????
Dennyus_distinctus_timjonesi_1     TAAGTCTTATTTAAATTCACCTTTTACCTGAGTATCAGGTGTTATTATTTTTTTTTTATTTATAGCAGCAGCTTTCCTAGGTTATGTCTTGCCTTGAGGTCAAATATCTTATTGAGGAGCAACTGTAATTACTAATTTAATTAGAGCCTTGCCTTACTTAGGAACTTTTTTAGTTGAGTGAG?TTGAGGAGGTTTTTCAGTTGTTAACCCAACTTTAACACGTTTTTTTTCTTTTCATTACCTAACTCCTTTACTTTCTTCTCTTTTTGTTTTTTTTCATTTATTTTTTTTACATGAAACAGGAAGAAGAAATCCCCTTGGACTTGGAAAAAATAGAGATAAAGTTTTTTTCCATCCTTTTTTTTCTTATAAAGACGTTCTTGGTTTTTTTTTTTTTTTTTTATTTTTATTTTTATTTGGATTAAAATTTCCTACTTTTTTT{AT}{AT}GGAT{CT}C{AG}{AG}A{AT}AATTTTTTAATTGCAAATCCAATA???ACGC?AGTTCATATTCA?CCTGA?
Dennyus_distinctus_timjonesi_2     TAAGTCTTATTTAAATTCACCTTTTACTTGAGTATCAGGTGTTATTATTTTTTTTTTATTTATAGCAGCAGCTTTCCTAGGTTATGTCTTGCCTTGAGGTCAAATATCTTATTGAGGAGCAACTGTAATTACTAATTTAATTAGAGCCTTGCCTTACTTAGGAACTTTTTTAGTTGAGTGAGTTTGAGGAGGTTTTTCAGTTGGTAATCCAACTTTAACACGTTTTTTTTCTTTTCATTATCTAACTCCTTTACTTTCTTCTCTTTTTGTTTTTTTTCATTTATTTTTTTTACATGAAACAGGAAGAAGAAATCCCCTTGGACTTGGAAAAAATAGAGATAAAGTTTTTTTCCATCCTTTTTTTTCTTATAAAGACGTTCTTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTAAAA??????????????????????????????????????????????????????????????????????????????
Dennyus_hirundinis                 TAAGTCCTACCTTAAGACACCCCTCACTTGAATAAGGGGGGTGGCACTCTATTTGCTTTTCATAGGAGTGGCGTTTCTGGGCTACGTCTTACCTTGGGGGCAAATATCTTACTGAGGGGGTACTGTAATTACCAATTTGATTAGTGCAGTGCCCTACTTCGGGCAGTCGCTGGTAGAATGAATTTGGGGGGGGTTTTCTGTGAGGGGCCCTACATTAACTCGATTTTTTACTCTCCACTACTTTTTACCCTTACTTAGGGTGGCATTTATTCTAGTCCACCTGACATTTTTACATAAGACGGGTAGATCAAACCCGTTGGGCTTGAGGAAAAACAGTGACAAGGTCTTTTTCCACCCATTTTTTTCCTATAAAGATTTTTTAGGGTTTAGATTTTTTGGACTACTCCTAATTTTTTTTAGGATAAAATATCCCAATCTCTTTCTTGATGCCGACAACTACAGCGTGGCTAATCCCATAACTACGCCTGCCCACATTCAACCAGAA
Dennyus_simberloffi                TAAATCCTACCTTTTCGC{AT}CCATTGACCTGAC???CCGGAG?AA??C????CCTGGC?TTTATAGCTGCAGCTTTTTTAGGGTACGT{AC}TTGCCTTGAGGTCAAATATCTTATTGAGGGGCAACTGTAATCACTAACTTAATTAGAGCTGTTCCTTATCTAGGAAACTCGTTAGTCGAGTGAATTTGAGGAGGGTTTAGTGTTGGAAGACCAACATTGACTCGATTTTTTACACTTCATTATATAACACCTTTATTAGGAAGAGGGATTGTAATAGTACACCTT????????ACACGAAACGGGAAGAAGAAATCCTCTTGGTCTTGGTAAAAATAGAGATAAGG?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Dennyus_singhi                     TAAATCTTATTTAAGTTCCCCCTTAACCTGAATTTCAGGTGTTTTTATTTTTTTTTTATTTATAGCAGCAGCTTTTTTAGGATATGTTTTACCTTGAGGTCAAATATCTTATTGAGGGGCAACTGTAATTACAAATTTAATTAGAGCCTTACCTTACTTAGGAGGTTTTTTAGTAGAATGAATTTGAGGTGGTTTTTCAGTTGGTAATCCAACTTTGACACGTTTTTTTTCTTTTCATTATTTAACTCCTTTACTTTCTTCTTTTTTTGTTTTTTTTCATTTATTTCTCTTACATAAGACAGGAAGGAGAAATCCTCTTGGACTTGGTAAAAATAGAGATAAAGTTTTTTTTCATCCTTTTTTTACTTTAAAAGATTTTTTCGGTTTTATTTTTTTTTTTTTCTGTTTGTTTTTTTTAAGGTTAAAATTTCCTACCTTTTTTTAGGTTCGGGAAAATTTTAAAATTGCAAATCCCATAACCACCACAGGTCACATTCAACCTGAA
Dennyus_somadikartai__U96418       TAAATCTTATTTAAATTCCCCTTTCACCTGAGGTTCAGGTGTTTTTTTTTTTTTTTTGTTTATAGCAGCAGCTTTTTTAGGTTACGTTCTTCCCTGAGGTCAAATATCCTATTGAGGGGCAACTGTAATTACAAATTTAATTAGAGCTTTCCCTTCCCTAGGAAGTTTTCTAGTAGAGTGAATTTGAGGAGGCTTCTCAGTTGGAAACCCAACTTTAACACGTTTTTTTTCATTCCATTATCTAACTCCCTTACTTTCTTTATTTCTTGTCTTGCTTCATTTATTTTTTTTACATGAAACAGGAAGGAGAAATCCTCTTGGACTTGGTAAAAACAGAGATAAAGTTTTTTTCCATCCTTTTTTTACTTTAAAAGACTTTCTTGGCTTTTTTTTTTTTGTTTTTTTTT{GT}GTTTTTTTTT???????????????????????????????????????????????????????????????????????????????????????
Dennyus_somadikartai_U96419        TAAATCTTATTTAAATTCCCCTTTTACCTGAGTTTCAGGTGTTTTTTTGTTTTTTTTATTTATAGCAGCAGCTTTTTTAGGTTACGTTCTTCCTTGAGGTCAAATATCCTATTGAGGGGCAACTGTAATTACAAATTTAATTAGAGCTTTACCTTACTTAGGAAGTTTTCTAGTAGAGTGAATTTGAGGAGGCTTCTCAGTTGGAAACCCAACTTTAACACGTTTTTTTTCATTCCATTATCTAACTCCCTTACTTTCTTTATTTCTTGTTTTTTTTCATTTATTTTTTTTACATGAAACAGGAAGGAGAAATCCTCTTGGACTTGGTAAAAACAGAGATAAAGTTTTTTTCCATCCTTTTTTTACTTTAAAAGACTTTCTTGGCTTTTTTTTTTTTGTTTTTTTTTGTTTTTTTTTTAGATGAAAAAATTGCCAAACTTTTTTAGATACTGACACTTTATTC??TGCTAATCCATTAGTCATA?????????????????????
Dennyus_thompsoni_U96424           TAAATCCTACCTTTTTACCCCAATAACCTGATCTATCGGAGTAAGACTATACCTGGCATTTATAGCAGCTGCTTTCCTAGGTTATGTTCTACCTTGAGGACAAATATCTTATTGAGGAGCTACTGTTATTACTAATCTTATTAGAGCAGTCCCATACTTAGGCAACTCATTAGTAGAATGAGTCTGAGGAGGTTTTAGTGTTGGCAGCCCAACTTTAACCCGATTTTTTACACTGCACTATATTACGCCTCTTTTAGGAAGATGTTTAGTTA??????ATTTATTTTTTTTACATGAAACAGGAAGAAGGAATCCTCTTGGTCTAGGAAAAAACAGAGATAAGATTTTTTTCCATCCTTTTTTTTCCTTTAAAGATTTAATTGGTTTTTTATTTTTTTTTTTTT?????????????????????????????????????????????????????????????????????????????????????????????????????
Dennyus_thompsoni_U96425           TAAATCCTACCTTTTTACCCCAATAACCTGATCTATCGGAGTAAGACTATACCTGGCATTTATAGCAGCTGCTTTCCTAGGTTATGTTCTACCTTGAGGACAAATATCTTATTGAGGAGCTACTGTTATTACTAATCTTATTAGAGCAGTCCCATACTTAGGCAACTCATTAGTAGAATGAGTCTGAGGAGGTTTTAGTGTTGGCAGCCCAACTTTAACCCGATTTTTCACACTGCACTATATTACGCCTCTTTTAGGAAGATGTTTAGTTATAATTCATTTATTTTTTTTACATGAAACAGGAAGAAGGAATCCTCTTGGTCTAGGAAAAAACAGAGATAAGATTTTTTTCCATCCTTTTTTTTCCTTTAAAGATTTAATTGGTTTTTTATTTTTTTTTTTATCCATCTTATTTTTTTGTTTAAAATTTCCTGTGGTGTTCCTGGATTCTGACAATTTTTTAATGGCTAATCCTATAGTTACGCCAGTTCACATTCAACCTGAA
Dennyus_vauxi                      TAAATCTTTTTTAAAATCTCCAATTACTTGATCAATTGGAGTTGCAATATATTTAATATATATGGCAGCAGCTTTTTTAGGTTATGTTTTACCATGAGGGCAAATATCATACTGAGGGGCAACAGTTATTACTAATTTATTAAGGGCAATTCCCTATATAGGACCGTTTTTAGTGGA?T?AATTTGGGGTGGATTTTCAGTTAGTAGGCCTACTTTAACTCGATTTTTTTCATTACACTATAGTCTTCCTCTAATTAGATTAGTTTTAATTATAACTCATTTAATTTTTTTACATGAAACAGGAAGATCAAATCCAATTGGATTAGGAAAAAATAGAGATAAAGTTATATTTCATCCTTACTTTACAATTAAGGATGTTATTGGTTTTATTCTTTTTTTAATTTTTTTATTTGTACTCTCTTTTAAACTTCCAAATTATTTTCTTGATTCTGATAATTTTTTAATTGCAAATCCTATAATTACTCCGGAACATATTCAGCCAGAG
Dennyus_wellsi                     TAAATCCTATCTTTTCTCTCCAATAACTTGGTTATCAGGAGTAAGACTATATCTTATTTTTATGGCAGCAGCTTTTTTAGGATACGTTTTACCTTGAGGGCAAATATCTTACTGAGGGGCCACTGTTATTACTAATTTAATTAGAGCTATTCCATATTTAGGTAGCTCATTAGTAGAATGAATTTGGGGGGGTTTCAGGGTTGGTAGGCCAACTTTAACTCGATTTTTTACACTACACTACATTACCCCTCTTATGGGAAGGTGTTTAGTAATAATTCATTTATTCTTTTTACATGAAACGGGGAGAAGAAACCCTCTGGGTTTAGGAAAAAACAGAGATAAGATTTTTTTTCATCCTTTTTTTTCTTTCAAAGATTTGATTGGTTTTATTTTTTTTTTTATGTTTTTTTTTTTTTTAGGTTTAAAGTTTCCCTTGGA???????????????????????????????????????????????????????????????????
Dennyus_wraggi                     TAAATCTTTTATCTCGTCCCCGTTGACTTGACTCTCTGGAGTAAGTTTATATTTAATTTTTATAGCTGCTGCTTTCTTAGGATACGTATTACCTTGAGGGCAGATATCTTATTGAGGGGCTACTGTTATCACTAACTTAATTAGAGCTGTCCCTTATTTAGGAAACTCGTTAGTCGAGTGAATTTGAGGCGGGTTTAGCGTGGGAAGTCCAACATTAACTAGATTCTTTACACTTCACTATATAACACCTTTGATAGGAAGAGGAGTTGTTATAGTACATTTATTTTTTTTACACGAAACGGGAAGAAGAAATCCTCTGGGTCTTGGTAAGAACAGGGATAAAGTTTTTTTTCATCCTTATTATTCTTTTAAAGACTTAATCGGGTTTTTTTTTTTTTTTTTCGTTTTTTTCGTAATAACTTTAAGGTTTCCTTTTTTTTCAAAGGTT?????????????????????????????????????????????????????????
;
END;