Fig. 2.

Neighbor-joining tree shows the ancient haplotypes that cluster in the two divergent lineages A and C. The number on the branch is the percentage of 2,000 bootstrap trees with the same branch structure. The four ancient goat haplotypes from southern France (red branches BO-A1, BO-A2, BO-C1, and BO-C2) are compared with 43 previously published modern goat sequences from local autochthonous breeds. Lineage A sequences are from contemporary goats from France (n = 14), Slovenia (n = 2), and Switzerland (n = 18). Lineage C sequences are from contemporary goats from Slovenia (n = 6) and Switzerland (n = 3). Lineage C has been identified only in the Slovenian goats and the Swiss Toggenburg goats; it has never been found in contemporary goats from France. Trees constructed by using Bayesian analyses give similar results (see Fig. 6).