Ancient European dog genomes reveal continuity since the Early Neolithic

Abstract

Europe has played a major role in dog evolution, harbouring the oldest uncontested Palaeolithic remains and having been the centre of modern dog breed creation. Here we sequence the genomes of an Early and End Neolithic dog from Germany, including a sample associated with an early European farming community. Both dogs demonstrate continuity with each other and predominantly share ancestry with modern European dogs, contradicting a previously suggested Late Neolithic population replacement. We find no genetic evidence to support the recent hypothesis proposing dual origins of dog domestication. By calibrating the mutation rate using our oldest dog, we narrow the timing of dog domestication to 20,000-40,000 years ago. Interestingly, we do not observe the extreme copy number expansion of the AMY2B gene characteristic of modern dogs that has previously been proposed as an adaptation to a starch-rich diet driven by the widespread adoption of agriculture in the Neolithic.

Figure 1. Phylogeny of ancient and contemporary canids.

(a) Phylogeny based on mtDNA. Age of the samples is indicated in parentheses, wolf samples are shown in orange. (b) NJ tree based on pairwise sequence divergence from whole-genome data.

Figure 2. PCA between ancient and contemporary canids.

(a) PCA of village dogs, with breed dogs and ancient dogs projected onto the PC space using SNP array data. (b) PCA of village dogs, breed dogs and ancient dogs using whole-genome SNP data ascertained in the New World wolves.

Figure 3. Genetic affinity of ancient samples.

Heat map of outgroup-f3 statistics of the form f3 (golden jackal; ancient sample; X) based on SNP array genotype data. Higher f3 values indicate increased shared drift between the samples, and therefore higher genetic similarities. (a) HXH shows greatest similarity with NGD and modern European village dogs (higher f3 values), and is most distant to East Asian and Indian village dogs. (b) CTC shares the most genetic similarity with HXH, followed by NGD and other European dogs. In addition, CTC shows greater similarity to village dogs from India (particularly unadmixed populations in the east) than HXH does. Outgroup-f3 statistic maps were created using the R packages ggplot2 and maps using the public domain Natural Earth data set.

Figure 4. Population structure between ancient and contemporary canids.

NGSadmix clustering for K=4 for village dogs, ancient dogs and Old World wolves based on the whole-genome SNP data.

Figure 5. Demographic model regarding ancient and contemporary dogs and wolves.

(a) The best model fit to both modern and ancient canid data using ADMIXTUREGRAPH on the whole-genome data set. This model had four f4-statistic outliers. Branches are indicated by solid black lines (adjacent numbers indicate estimated drift values in units of f2 distance, parts per thousand), whereas admixture is indicated by coloured dashed lines (adjacent numbers indicate ancestry proportions). Sampled individuals/populations are indicated by solid circles with bold outline. Wolves are labelled as ‘wolf’ and dogs are labelled according to their continental origin. (b) Divergence times of contemporary dogs and wolves inferred using G-PhoCS. Mean estimates are indicated by squares with ranges corresponding to 95% Bayesian credible intervals. Migration bands are shown in grey with associated value representing the inferred total migration rates (the probability that a lineage in the target population will migrate into the source population). The divergence time for HXH and NGD and modern European dogs is inferred using a numerical approach. The proportion of Indian village dog ancestry in CTC is inferred by NGSadmix and the proportion of South China village dog ancestry in HXH and NGD is inferred by f4-ratio test, shown in red.

Figure 6. Haplotype and copy number variation at the amylase 2B (AMY2B) locus.

(a) Genotype matrix of selected sites within F_ST-derived domestication locus 12 (chr6: 46854109-47454177). SNP genotypes are represented as either homozygous for the reference allele (0/0; blue), heterozygous (0/1; white) or homozygous (1/1; orange) for the alternate allele. The positions of AMY2B (green line) and RNPC3 (model above) are indicated. (b) Read-depth-based estimation of AMY2B copy number for the Andean fox (light green), golden jackal (light green), coyotes (dark green), wolves (orange), ancient samples (red), village dogs (purple) and breed dogs (blue). Dashed line indicates diploid copy number of two.