Mitochondrial phylogeography is a useful tool for the study of wild populations 1. But applying phylogeography to domestic species is more complicated. For example, the arrival of dogs into the New World was not a simple expansion of Asian dog populations, but a consequence of human migrations 2. Humans have a history of population movements and social changes over the last ten thousand years 3456, and this, together with the human-mediated breeding history has affected the genetic composition of livestock animals 7. Therefore, human influence cannot be neglected when studying patterns of genetic diversity in domesticates.

A classic example of the use of mitochondrial DNA (mtDNA) diversity to infer the history of domestication refers to dogs (Canis familiaris). Four to six mitochondrial haplogroups (Hg) have been described in genetic studies of modern dogs 8, indicating recurrent domestication or backcrosses between domestic dogs and wild wolves (Canis lupus). Three of the major Hgs are distributed throughout the world, whereas one (D) is restricted to Europe, especially in breeds originating in Scandinavia 891011. Similar patterns of fragmented genetic diversity have been used to argue for local domestication in other species 12. Such scenario could apply to dogs as they appear as early as 9000 years ago in Scandinavia 1314, and as dogs and wolf remains have been found on the same sites 1516.

We have genetically typed mtDNA from ancient Scandinavian dog remains to investigate whether the high frequency of a rare dog Hg in northern Europe is evidence of a local domestication event. We predict that an early domestication event in Scandinavia would be visible in a notable frequency of Hg D in ancient Scandinavian dog remains.

Reproducible sequence data for the full 219 bp sequence was recovered from 18 samples. The remaining six specimens only yielded reproducible sequence data for a shorter 107 bp product (DQ860843-3 DQ860864, AY673648–AY673672, Table 1). Phylogenetic reconstruction including the 18 prehistoric dogs that yielded complete sequences and 543 modern dog sequences 11 revealed that all prehistoric dogs grouped within modern Hgs (Figure 1). Seven of the 18 sequences belonged to Hg A, the group that encompasses more than 70% of all tested modern dogs around the world 11, while the remaining eleven belonged to the now rare Hg C. Previously published data on 273 Swedish dogs indicated frequencies of the four major Hgs: A 69.2%, B 18.3%, C 7.0%, and D 5.5% 9. When only native Scandinavian breeds were considered (n = 54), the haplotype frequency for Hg D increased to 33.3% 9. A comparison of the 219 bp sequences obtained from the ancient dog specimens (n = 18) and the contemporary native breeds indicates that the frequency of Hg D is significantly reduced in the ancient data set (0% in the ancient dataset, 33% in the modern dataset, p < 0.001). The remaining six ancient Scandinavian dogs that yielded only 107 bp of reproducible sequence data, also indicated an absence of Hg D (Table 2). In total, eleven sequences had substitution patterns indicative for Hg A, while the remaining 13 had a substitution indicative for Hg C (Table 1).

When the complete ancient dataset was compared to the contemporary dataset, it proved equally improbable (p < 0.001) that Hg D was present in the oldest specimens in a frequency similar to that observed in modern dogs. Using a binomial distribution, we estimate that the frequency of Hg D must have been lower than 0.118 in the original population for us not to have noticed it in 24 samples (p < 0.05), and lower than 0. 182 during the Neolithic for us not to have noticed it in 15 samples (p < 0.05). Lastly, the χ² test between the Hg frequencies of the complete ancient dataset with that of the complete Scandinavian (not only considering native breeds) demonstrated a significant deviation between the modern and ancient frequencies (p < 0.0388, χ² = 4.27, df = 1).

Our results indicate that Hg frequencies have been altered in Scandinavian dogs since their first arrival. Interestingly, while Hg C is overrepresented in our ancient material, there is a complete lack of the Scandinavian group D in our ancient dataset. Hg D is the one that could support a Scandinavian origin whereas Hg C is suggested to be of Asian origin 11. Thus, we find no obvious evidence for prehistoric canid domestication in Scandinavia. An external origin of Scandinavian dogs is supported by morphologic data, as even the oldest remains of dogs in Scandinavia were of smaller size than those of prehistoric and extant wolves 1517. While canid domestication may have occurred in other parts of Europe 18, Scandinavian dogs were likely imported and had experienced a long period of morphological change under human control before they reached the Scandinavian peninsula.

In a wider context, our data calls for caution when using modern sequences of domestic animals to interpret the history of domestication. There is a profound difference on selective forces on wild and domestic animals. Domesticates are subject to constant manipulation and follow the same historic vicissitudes as the associated human population. For example, genetic diversity may change rapidly due to intense selective breeding, backcrossing with the wild ancestor 19202122, migration of human groups with genetically different domesticates 2, and decimation of local populations by invaders 23. Hg frequency could change over a short period of few generations. While diversity and branching pattern of mitochondrial DNA may be used to study the number and possible antiquity of domestication events, phylogeographical patterns in domestic species may indeed not be suitable to base discussion on their geographical origin. Close collaboration between zooarchaeologists and molecular biologists, involving the study of ancient specimens, may be the only way to verify the continuity through time of the species that have set the basis of our culture.

We analysed sequences from 24 archaeological domestic dogs. The skeletal material represents eight Scandinavian sites: four Neolithic (≈5300–4500 BP) and four Medieval (≈1000–500 BP) (Table 1, Figure 2). DNA was extracted, PCR-amplified and sequenced according to previously published protocols 2425 (Table 1). A subset of the sample sequences (n = 7) was replicated in an independent laboratory (Center for Ancient Genetics, University of Copenhagen) confirming the original results in all cases. The new data was combined with previously published data 2425 for analysis (see Table 1). Most of the Neolithic samples, those from Ajvide, Visby, and Korsnäs (Figure 2), were recovered as isolated findings in cultural layers. One sample was from a complete skeleton found in a burial in Central Sweden (Bergsgraven in Linköping). The Medieval samples originated from isolated skeletal remains recovered in urban (Skara and Stockholm) or rural contexts (Eketorp, Sunnerby).

We used polymorphisms found within a 219 bp fragment of the dog D-loop region and comparison with previously published sequences to determine Hgs. To portray the relationship between sequences we constructed a reduced median network, including all 219 bp, using Network 4.1 26; threshold was set to 1. The default parameters for reduction were used, where parallel mutations are assumed to be more frequent between existing sequences, than between an existing sequence and a median vector. As the reduction was intense, a NJ tree was constructed to support the network using the Kimura 2-parameter model of sequence evolution. Support for the nodes was assessed with 1000 bootstrap pseudoreplicates.

The Hg frequencies within the ancient datasets were compared to those in modern Scandinavian dogs 9 using χ² tests. To ensure a minimum sample of 5 for all cells in χ² tests, we pooled Hgs A and D, and C and B (following the best natural grouping according to the network, Figure 1). Finally, we used the binomial distribution to estimate the probability of observing as many sequences from Hg D as found in the ancient samples assuming that the relative frequency was the same as in modern native Scandinavian dogs.

HM did all experimental work apart from the independent replications, and helped analyse the data and write the paper. CV did part of the analytical work, and helped write the paper. TG and EW did the independent replication. TG revised the language. JS did the morphological selection, and described the archaeology. GH supervised the experimental work. AG did the analytical work together with HM and CV, and wrote the paper together with HM and CV. All authors read and approved the final manuscript.