DOI: 10.5061/dryad.547d7wmj1
title: Tracing 600 years of long-distance Atlantic cod trade in medieval and post-medieval Oslo using stable isotopes and ancient DNA

description: Marine resources have been important for the survival and economic
 development of coastal human communities across northern Europe for
 millennia. Knowledge of the origin of such historic resources can provide
 key insights into fishing practices and the spatial extent of trade
 networks. Here, we combine ancient DNA and stable isotopes (δ13C, δ15N,
 non-exchangeable δ2H, and δ34S) to investigate the geographical origin of
 archaeological cod remains in Oslo from the eleventh to seventeenth
 centuries CE. Our findings provide genetic evidence that Atlantic cod was
 obtained from different geographical populations, including a variety of
 distant-water populations like northern Norway and possibly Iceland.
 Evidence for such long-distance cod trade is already observed from the
 eleventh century, contrasting with archaeological and historical evidence
 from Britain and other areas of Continental Europe around the North and
 Baltic Seas, where such trade increased during the thirteenth to
 fourteenth centuries. The genomic assignments of specimens to different
 populations coincide with significantly different δ13C values between
 those same specimens, indicating that multiple Atlantic cod populations
 living in different environments were exploited. This research provides
 novel information about the exploitation timeline of specific Atlantic cod
 stocks and highlights the utility of combining ancient DNA methods and
 stable isotope analysis to describe the development of medieval and
 post-medieval marine fisheries.
description: # Tracing 600 years of long-distance Atlantic cod trade in medieval and
 post-medieval Oslo using stable isotopes and ancient DNA This repository
 contains the data analysis performed for the publication: *Tracing 600
 years of long-distance Atlantic cod trade in medieval and post-medieval
 Oslo using stable isotopes and ancient DNA* by Martinez-Garcia, Pulido et
 al., 2024 The repository contains the following files: ###
 Martinez-Garcia\&Pulido.2024.Medieval\_cod\_trade\_Oslo\_ancientDNA\_Isotopes.R: An R script that performs all statistics presented in figures and tables in the paper: *"Martinez Garcia&Pulido.2024.Medieval_cod_trade_Oslo_ancientDNA_Isotopes.R"* This script will read all the files in the "Input_files" folder to perform the different statistical analyses presented in the paper, as well as the plots in the main text and supplementary material.Annotations are provided throughout the script through libraries and dataset loading, cleaning of the data, and analyses and plotting. ### Input\_files A folder with output files obtained from the sequencing data and the isotopic analyses of the bone material. These files are used in the R script presented above. We have analysed 106 Atlantic cod bone samples collected from two archaeological sites in Oslo. Samples –cranial and postcranial elements– were morphologically (see Archive: Osteological collections, University Museum, University of Bergen) and genetically identified as Atlantic cod. Stable isotope analysis was performed on 100 Atlantic cod specimens (50 of which were also processed for genomic sequencing). The following files are the output of the isotopic as well as genomic analyses, as follow: #### MASTER\_isotopes.genotype\_LMG.txt Results after measuring stable carbon (δ13C), nitrogen (δ15N), non-exchangeable hydrogen (δ2H, and sulfur (δ34S) on purified bone collagen. The content of the table are as follows: * aDNA_ID: ID assigned for the genomic data. * Old_ID: Original ID assigned at the moment of sampling. * Bone_Element: Bone element determined morphologically. * Layer: Fire layer where the bone element was sampled. * Age: Estimated age of the sample based on archaeological context (e.g., fire layer) including carbon-14 dating, dendrochronology, and typology. Age is estimated in the approximate century the sample originated from, years of the common era (CE). * Size: Estimated body size of the sample determined from morphological analyses of the bone element. Units=centimeter. * d13C, d15N: Isotopic values of Carbon and Nitrogen isotopes from purified bone collagen. For δ13C values and δ15N values, the extracted collagen was analysed in triplicate at the Godwin Laboratory, Department of Earth Sciences, University of Cambridge, using a Costech elemental analyser coupled to a Thermo Finnigan Delta V Isotope Ratio Mass Spectrometer (IRMS). All isotope data are reported using international scales: δ13C values are reported relative to VPDB, and δ15N values to AIR. * Mean.Hydrogen.Content: non-exchangeable hydrogen (δ2H). The non-exchangeable hydrogen represents in vivo values rather than the exchange with atmospheric water vapor. For δ2H values (measured by Iso-Analytical Limited, by elemental analyser IRMS), analyses were routinely in duplicate, although some samples yielded only enough collagen for single measurements. All isotope data are reported using international scales: δ2H values to VSMOW. * Meand2HV-SMOW.corrected: The reported non-exchangeable δ2H values are corrected for exchangeable hydrogen by three-point linear calibration using standards. * Mean.Sulfur.Content: For δ34S values, (measured by Iso-Analytical Limited, by elemental analyser IRMS), analyses were routinely in duplicate, although some samples yielded only enough collagen for single measurements. All isotope data are reported using international scales: δ34S to VCDT * C.N_ratio: Atomic ratio between Carbon and Nitrogen: Used for appropriate quality-control thresholds (atomic C/N ratio of 2.9 – 3.6) * C.S_ratio: Atomic ratio between Carbon and Sulfur: Used for appropriate quality-control thresholds (atomic C/S ratio of 125 – 225). * N.S_ratio: Atomic ratio between Nitrogen and Sulfur: Used for appropriate quality-control thresholds (atomic N/S ratio of 40 – 80). * LG01 LG02 LG07 LG12: These columns contain the Happlotipe identification for the corresponding Inversion in Linkage group 01 (LG01), LG02, LG07 and LG12. * LofotenSkrei LofotenCoastal NorthSea Oresund IrishSea Iceland IcFrontal IcCoastal WestCoast northcentral and northernmost: Likelihoods of belonging to these populations, determined by the BAMscorer pipeline. * population.assigment: Final population assignment taking as criteria the highest probabilities. #### Paleomix\_summary.txt This file contains the results produced by PALEOMIX v1.2.13, which summarize statistics that allow for the quality of the reads sequenced. The table is structured as follows: * ID: sample ID * Pair: Total number of paired reads. * Clonality: measured as the fraction of the mapped reads that are duplicates. * Frac: Endogenous DNA content (defined as the unique, nonrepetitive fraction of reads aligning toward the reference genome with a minimum MapQ value of 25). * Hits_nu: number of reads mapped to the reference genome. * Nu_coverage: fold coverage obtained for the nuclear genome. * Length: the average insert length in base pairs. * Locality: Fire layer in which each individual was sampled. To determine the biological origin of Atlantic cod specimens we the BAMscorer pipeline which generates probability assignments on the major chromosomal inversions in Atlantic cod (LG1, LG2, LG7, and LG12). The results and corresponding probabilities are found respectively in the following files: #### InversionCaller\_LG01.txt The contents of this table are as follows: * aDNA_ID: Sample ID * Locality: Fire layer in which each individual was sampled. * Clonality: measured as the fraction of the mapped reads that are duplicates * Frac: Endogenous DNA content (defined as the unique, nonrepetitive fraction of reads aligning toward the reference genome with a minimum MapQ value of 25). * AA BB AB: genotype probabilities. * SNPs: Number of SNPs used to calculate the genotype probabilities The files corresponding to the other inversions in linkage groups 2 (LG02), 7 (LG07), and 12 (LG12) follow the same pattern as above. #### LG01\_counts.txt Number of individuals presenting a corresponding genotype (AA, AB, or BB) for the inversion in Linkage Group 01 (LG01). The count is made after filtering genotypes that are supported by less than 5 SNPs. The tables LG02_counts.txt, LG07_counts.txt, and LG12_counts.txt, follow the same structure as that of LG01_counts.txt, presented above. #### Probability\_ancient.genotypic.affinity\_FoodImpact.txt This table contains the probability of each sample belonging to the genotype presented to the following populations, as described in the main paper. For each individual specimen, the source population with the highest percentage (%) has been considered as its most likely geographical population source: Lofoten.Skrei, Lofoten.Skrei, North.Sea and Oresund. The table is structured as follows: * Locality: Fire layer from which the bone sample was located. * Sample: Sample ID of each individual. * probability: Probability of the most likely geographical population source. * type: most likely geographical population source. Finally, genotypes from the different inversions and their probability scores are summarized and paired with the metadata information (bone element, stratigraphic layer, Age, and body size) of each individual, in the following table: #### All\_genotypes.txt All columns of the table describe the measurements and factors described above.