Our results ensued from 116 Neolithic specimens, a relatively large number for an ancient DNA study, thus enabling us to perform sensible statistical modelling. To the best of our knowledge, our study has been the first to develop a quantitative model to assess the prehistoric origin of mtDNA haplotypes of northern domestic pigs. However, for precise estimation of the model parameters, the study sample size may have been only moderately sufficient, as is evidenced by the relatively large confidence intervals obtained. Nevertheless, a clear trend is apparent. For early period t 2 , our analysis suggests none or only little influx of wild boar from the north. Thus, whereas predominant maternal descent from southern domestic pigs is likely, it cannot be excluded that a minor proportion of pigs received their mtDNA from animals from the northern region. The confidence interval for p NG (the probability that the mtDNA of a northern t 2 domestic pig derived from a northern t 1 wild boar) was smaller in the four-haplotype model, not least owing to the larger amount of information that was taken into account, so that the parameter estimates of the four-haplotype model can be assumed to be more accurate than those of the two-haplotype model. Qualitatively, however, the two- and four-haplotype models agreed well for both time periods, thereby increasing confidence in our results.

Previous zooarchaeological research suggests that domesticated pigs were first exploited in northern Europe at around 4100 BC8. According to a recent aDNA study, however, domesticated Near Eastern lineage animals may have been present in the region several centuries earlier, a result derived from a directly radiocarbon-dated specimen with haplotype Y1 (two sigma range: BC 4720–4582)2. The mtDNA results presented here further suggest that, during the early time period t 2 (5000–4000 BC), female domestic pigs were introduced almost exclusively from the south. In the following time period t 3 (4000–3000 BC), by contrast, imports from the south contributed little to the northern mtDNA genetic pool and, consequently, the mtDNA of northern European lineage domestic pigs should have originated mainly from local animals, a substantial proportion (between 43% and 100%) of which were wild boars. Our model highlights a clear shift in suid management strategies after 4000 BC, a pattern in agreement with the model generated by Larson et al.1, which drew from a much smaller and geographically more widespread sample. Based on the occurrence of Near Eastern haplotype Y1 as late as t 3 (between 4000 and 3000 BC; Tables 1 and 2) it seems that, at least in the north, the replacement of Near Eastern mtDNA haplotypes by European ones could have taken longer (>500 years) than previously suggested1. Equally intriguing, our study revealed a high level of interbreeding between the early domestic northern populations and local wild boars. Notably, significant post-domestication gene flow from wild animals into managed swineherds is further corroborated by a recent genomic study on modern pigs9.

Why did early agriculturalists in northern Europe change their suid management strategy after 4000 BC? It may be that the availability of domesticated Near Eastern pigs in the earliest Neolithic settlements located in northern Europe was initially limited, reflecting their location at the end of the Neolithic ‘supply chain’. The reliability of Near Eastern-derived livestock was perhaps also unstable, particularly if pig husbandry strategies applied to Near Eastern domesticates initially failed to adjust for northern European environments and dietary conditions. The overall number of domestic pigs carried to the north by the first Neolithic agriculturalists along with their livestock may have been relatively small. As a case in point, domesticated sheep and goats, core constituents of the Near Eastern Neolithic livestock package, were also exploited at low intensities only in the earliest Neolithic settlements of the southwestern Baltic region, with their remains generally comprising no more than 10% of the faunal assemblage10,11 [Makarewicz, unpublished data]. A small domestic source population would have been susceptible to isolation, disease and over-harvesting which would have made it difficult to maintain a stable and viable swine herd. In addition, the material cultural record indicates that the contact between northern and southern European cultures was only sporadic at the time8,12. If this was the case, then the strategy of interbreeding locally abundant female wild boars with domestic males would have facilitated an increase in swine herd size without having to rely upon a limited and uncertain supply of Near Eastern domesticated pigs from the south. Moreover, local stock are usually well adapted to their specific environmental conditions, for instance, by showing greater resistance to endemic pathogens13. Out-crossing therefore may have produced more resilient, fertile and larger offspring12,13. Another explanation for the dominance of local European mtDNA genomes in later pig specimens could be that the corresponding genomes conferred a selective advantage in the north, for example, in terms of energy metabolism that would eventually lead to their fixation in European domesticates.

It has been suggested before that interbreeding between pigs and wild boars was mainly unintentional and resulted from chance encounters due to escaped feral domesticates, loose swine management systems and mobile swine herding9,12. Loose pig husbandry is thought to have been characteristic of European agricultural systems for millennia14. However, this scenario would not explain the introgression of European wild sow mtDNA haplotypes (i.e. of female animals) into expanding Neolithic swineherds; mating between domesticated female sows and European wild boars would not have changed the mtDNA pool of domestic herds. The latter instead would have required the incorporation of additional wild females, which could, for instance, be achieved by capture of wild female piglets as part of an active herd-building strategy. Therefore, a combination of loose management and intentional integration of female wild boars seems to have occurred.

The results of our quantitative analyses strongly suggest that pig management was an ever-evolving process which depended heavily upon interbreeding domesticated animals with local wild boar, in particular wild sows. This insight demonstrates how a change in animal handling ~6000 years ago may have influenced livestock composition up to the present day. What is more, our mathematical model presented here can also be adapted to other proxies (i.e. animals) and haploid DNA markers as well as scenarios and periods.