Fig 1.
The neighbor-joining tree of Japanese Shorthorn mtDNA complete D-loop sequences.
The tree was constructed with representative sequences of the mtDNA haplogroups (T1–T4, I1–2 and P).
Fig 2.
Sequence variation observed among 122 Bos samples with haplogroup P.
The samples were from 86 modern cattle (83 Japanese Shorthorn, two Korean cattle, and one Chinese Holstein) and 36 archaeological aurochs. They were aligned with BRS (V00654) using the hypervariable 410 bp (bp 15903–16313). Sequence codes and numbers are given in the first column. Only variable sites, with sequence positions given above, are shown. Identity with the first sequence is denoted by a dash substitution by a different base letter. The haplogroup P of European aurochs (Pa) and modern Asian cattle (Pc) were defined by the network analysis shown in Fig 3. 1HT: haplotype using the hypervariable 410 bp sequence.
Fig 3.
A reduced median network of mtDNA haplogroup P using the hypervariable 410 bp.
The network was constructed from 122 Bos samples (86 modern cattle samples: 83 Japanese Shorthorn, two Korean cattle, and one Chinese Holstein, and 36 archaeological aurochs samples). The number of times each variant is represented is proportional to the area of its circle. Lines connecting sequence nodes denote substitutions. Numbers with red color indicate substitution positions. Small red circles represent hypothetical sequences which have not been found in the sequencing exercise.