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Populations can adapt to novel selection pressures through dramatic frequency changes in a few genes of large effect or subtle shifts in many genes of small effect. The latter (polygenic adaptation) is expected to be the primary mode of evolution for many life-history traits but tends to be more difficult to detect than changes in genes of large effect. Atlantic cod (Gadus morhua) were subjected to intense fishing pressure over the twentieth century, leading to abundance crashes and a phenotypic shift toward earlier maturation across many populations. Here, we use spatially replicated temporal genomic data to test for a shared polygenic adaptive response to fishing using methods previously applied to evolve-and-resequence experiments. Cod populations on either side of the Atlantic show covariance in allele frequency change across the genome that are characteristic of recent polygenic adaptation. Using simulations, we demonstrate that the degree of covariance in allele frequency change observed in cod is unlikely to be explained by neutral processes or background selection. As human pressures on wild populations continue to increase, understanding and attributing modes of adaptation using methods similar to those demonstrated here will be important in identifying the capacity for adaptive responses and evolutionary rescue.This article is part of the theme issue ‘Detecting and attributing the causes of biodiversity change: needs, gaps and solutions’.

Peer reviewed: True, Funder: McDonald Institute for Archaeological Research, Mediaeval walrus hunting in Iceland and Greenland-driven by Western European demand for ivory and walrus hide ropes-has been identified as an important pre-modern example of ecological globalization. By contrast, the main origin of walrus ivory destined for eastern European markets, and then onward trade to Asia, is assumed to have been Arctic Russia. Here, we investigate the geographical origin of nine twelfth-century CE walrus specimens discovered in Kyiv, Ukraine-combining archaeological typology (based on chaîne opératoire assessment), ancient DNA (aDNA) and stable isotope analysis. We show that five of seven specimens tested using aDNA can be genetically assigned to a western Greenland origin. Moreover, six of the Kyiv rostra had been sculpted in a way typical of Greenlandic imports to Western Europe, and seven are tentatively consistent with a Greenland origin based on stable isotope analysis. Our results suggest that demand for the products of Norse Greenland's walrus hunt stretched not only to Western Europe but included Ukraine and, by implication given linked trade routes, also Russia, Byzantium and Asia. These observations illuminate the surprising scale of mediaeval ecological globalization and help explain the pressure this process exerted on distant wildlife populations and those who harvested them.

Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate- to high-coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low-coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole-genome data. We scored both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage data (as low as 0.0001x) based on genome-wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.

Figure S1. Cha��ne op��ratoire typology entailing sets of increasingly elaborate steps used to remove and sculpt medieval walrus rostra found in Greenland and Europe. The Kyiv specimens have been classified using this scheme. Type 1 rostra were only modified by cut marks made during removal from the skull. In type 2, the tusk alveoli were thinned by rough parallel cuts that faceted the surface of each socket. Type 3 rostra also exhibit decorative carving of the nasal aperture. In type 4 the tusk sockets are smoothly rather than roughly facetted and the ventral margin between the tusks is always carved. Fragmentary rostra lacking some information can be attributed to broader categories (e.g. type 2/3). Image reproduced from Figure 2 of Barrett et al. (2020), where it was published open access under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Figure S2. Distribution of medieval European finds of walrus rostra that have been genetically analysed. Potential medieval trade routes are also shown. Mitogenomic clade assignment is indicated for each specimen. Stars mark the locations of control samples from Greenland, Iceland, Finnmark and Svalbard. The modern distributions of the eastern and western genetic clades of Atlantic walrus are shaded. Base map after Barrett et al. (2020) and references therein.

Supplementary Figure S1, S2 and S3 illustrating in-detail the results obtained in this study.

Supplementary Figures and Tables S1, S2 and S3