Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany

Abstract

Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15-46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800-1066 CE) and subsequent medieval (1066-1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.

Keywords: chromosomal inversion; fish bone; genomics; high-throughput sequencing; trade.

Fig. 1.

Approximate sampling locations of Atlantic cod in the northern Atlantic region in Europe. (A) Atlantic cod (Gadus morhua) specimens (sample size is indicated between brackets) were obtained from modern populations (black) and archaeological excavations (red). The NEA sample was obtained in winter, when this population migrates southwards from the Barents Sea to the Lofoten Archipelago to spawn. The Lofoten population was sampled during summer when the NEA cod are absent from this region. The modern range of Atlantic cod is indicated by blue shading. (B) Archaeological Atlantic cod jaw-bone (premaxilla) from Orkney.

Fig. S1.

aDNA fragmentation and misincorporation patterns of sequencing read data from 15 Atlantic cod samples. Patterns were obtained by using MapDamage v. 2.0.6 after down-sampling BAM files to 1 million reads. For visualization purposes, we only show the typical increase in C > T misincorporations due to cytosine deamination at the 5′-end of DNA fragments and the corresponding increase of G > A misincorporations at the 3′-end.

Fig. 2.

Genetic population structure in 183 Atlantic cod specimens. (A) PCA based on 99,819 SNPs. Ancient specimens (stars) were projected onto the first two principal components calculated by using individuals from modern populations (circles). (B) ADMIXTURE ancestry components (k = 2) for modern and ancient specimens. The width of the bar for ancient specimens is widened to aid visualization. LG01, 02, 07, 12, and unplaced scaffolds were excluded from these analyses (Results for explanation).

Fig. S2.

ADMIXTURE ancestry components for modern and ancient Atlantic cod specimens. Population structure was investigated by using models with a variable number of clusters (k). Model fit was assessed by calculating the CV error, with a lower CV error indicating a better fit. LG01, 02, 07, 12, and unplaced scaffolds were excluded from these analyses (see Results for explanation).

Fig. 3.

Spatial genomic variation in megabase-scale inversions in Atlantic cod. (A) Allele frequency distribution of four inversions (on LG01, 02, 07, and 12) in four modern populations. The collinear allele (gray) and inverted allele (yellow) segregate as biallelic loci. (B) Individual inversion genotypes of ancient Atlantic cod. The collinear (gray, AA), inverted (yellow, BB), and heterozygote (yellow/gray, AB) genotypes segregate independently on four chromosomes. (C) Genotypic affinity of ancient specimens. The overall probability of obtaining the ancient individual’s composite genotype was calculated by binomial sampling of inversion genotypes from the respective allele frequency distributions of the four modern populations.

Fig. S3.

PCA of genomic inversions in Atlantic cod. Ancient specimens (stars) were projected onto the first two principal components calculated by using individuals from modern populations (circles). The first principal component (PCA 1) separates genomic variation within each of the 4-Mbp-long regions (LG01, 9.1–26.2 Mbp; LG02, 18.5–24 Mbp; LG07, 13.6–23 Mbp; LG12, 1.3–13.6 Mbp) into distinct clusters (gray dotted ovals) that reflect the biallelic segregation of the three major inversion genotypes (AA, collinear; AB, heterozygote; BB, inverted). The number of SNPs (n) used per region is indicated. Mean heterozygosity values per genotype (presented in gray under each genotype; estimated by calculating the inbreeding coefficient F using a method of moments as implemented in VCFTOOLS v0.1.14) show the marked decrease in F values for the AB genotypes due to heterozygote excess. Ancient samples follow the trimodal cluster pattern of the modern individuals.