Tree of Complete Bovine mtDNA Sequences Belonging to Haplogroup T1.

<p>This tree was built as previously described <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone.0038601-Achilli1" target="_blank">[8]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone.0038601-Bonfiglio1" target="_blank">[11]</a>. The position of the Bovine Reference Sequence (BRS) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone.0038601-Anderson1" target="_blank">[23]</a> is indicated for reading off-sequence motifs. Divergence time estimates are those obtained using ML as reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone-0038601-t003" target="_blank">Table 3</a>. Branches display mutations with numbers according to the BRS; they are transitions unless a base is explicitly indicated for transversions (to A, G, C, or T) or a suffix for indels (+, d) and should be read as if the BRS was an artificial root. Recurrent mutations are underlined; back mutations at positions that separate the T1 tree from the BRS are prefixed with the superscript @. Note that the reconstruction of recurrent mutations in the control region is ambiguous in a number of cases. Heteroplasmy is marked with a suffix (h). The numbering of sequences is the same as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone-0038601-t002" target="_blank">Table 2</a>. The orange line connecting T1e and T1f to nps 16050 and 16113 reflects the uncertainty of their classification as quasi-sister taxa of sub-haplogroups T1a to T1d and implies the possibility that either one or the other or both might well descend from a T1′2′3′ – T1 intermediate (see Discussion for more details). Note that a potential affiliation of sequence #44 within sub-haplogroup T1e should be also considered (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#s2" target="_blank">Results</a>). The pie charts summarize the typing results of the survey performed on our entire dataset of 281 T1 mtDNAs (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone-0038601-t001" target="_blank">Table 1</a>) with diagnostic T1 sub-haplogroups markers. The numbers of mtDNAs for each sub-haplogroup are shown and include the 54 mtDNAs completely sequenced in this study, but not those previously published (#3, 4, 10, 22, 23, 29, 37, 46, 49 and 62) (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038601#pone-0038601-t002" target="_blank">Table 2</a>). Colors in the pie charts indicate geographical origins.