A series of maps depicting the shifting geographic positions of European and Near Eastern pig haplotypes over the past 13,000 years. (A and B) (A) Bayesian (Monte Carlo–Markov chain) consensus tree of 112 modern wild Sus mtDNA control region haplotypes rooted by a common warthog (Phacochoerus aethiopicus). Red, orange, and yellow represent three clusters on the tree that correspond to specific regions on the map in B (Europe, Italy, and the Near East, respectively), where the majority of pigs possess haplotypes within that cluster. Posterior probabilities of the major nodes are listed for each of the branches. (C–F) Time series of maps identifying the locations of ancient pig samples from which DNA haplotypes were generated within Europe. Each symbol corresponds to a single sample, and the colors correspond to those used in A and represent the cluster on the tree to which the samples belong. The four Near Eastern haplotypes discussed in Results and Discussion (Y1, Y2, A1, and A2) are represented by yellow circles, squares, asterisks, and triangles, respectively. Numbers to the right of sample locations in C represent approximate sample ages (in calibrated years B.C.).“Bercy” and “Eilsleben” in D refer to specific sites, and “Romania” refers to several sites discussed in Results and Discussion. Clustered symbols represent multiple samples from the same or geographically proximate sites. The upper and lower blue lines represent the Rhine and Danube rivers, respectively. The dotted yellow arrow in D depicts the hypothesized Danubian trajectory along which the Y1 haplotype was transported, and the dotted red arrow in F highlights the movement of European domestic pigs transported into Armenia. The question marks at the origins of the arrows reflect the uncertainty regarding the precise locations from where the dispersal routes began. C–F very broadly represent the European Mesolithic, the European Neolithic, the Bronze Age, and all subsequent ages to the medieval period, respectively. Additional details regarding all of the modern and ancient samples used in this study can be found in SI Discussion.