Tree of mitogenomes from Egyptian cattle.

<p>Sequences #1–19, #25, #30–31 have been determined in this study, while sequences #20–24 and #26–29 were previously reported [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141170#pone.0141170.ref027" target="_blank">27</a>]. GenBank accession numbers are reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141170#pone.0141170.s002" target="_blank">S1 Table</a>. This tree was built as previously described [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141170#pone.0141170.ref022" target="_blank">22</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141170#pone.0141170.ref024" target="_blank">24</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141170#pone.0141170.ref027" target="_blank">27</a>]. The hypervariable insertion of a G at np 364, the length variations in the C tract scored at np 221 and the A tract scored at np 1600 were not used for the phylogeny construction. The position of the Bovine Reference Sequence (BRS) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141170#pone.0141170.ref036" target="_blank">36</a>] is indicated for reading off-sequence motifs. 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 heteroplasmy (h). Recurrent mutations within the phylogeny are underlined and back mutations are marked with the suffix @. Note that the reconstruction of recurrent mutations in the control region is ambiguous in a number of cases. The pie charts summarize haplogroup frequencies in the Menofi (green) and Domiaty (orange) breeds.