Harmonized microsatellite dataset for circumpolar populations of reindeer and caribou (Rangifer tarandus)

This repository contains a harmonized microsatellite genotype dataset and associated validation statistics for circumpolar populations of reindeer and caribou (Rangifer tarandus). The dataset was compiled from previously published population genetic studies conducted in Alaska, Canada, and Russia and subsequently standardized to enable joint analysis across regions. Because the original datasets were generated in different laboratories and genotyped using different electrophoretic platforms, systematic allele-size offsets among datasets were addressed using a reference-based mode-shift harmonization procedure. In this procedure, allele sizes were adjusted by applying locus- and dataset-specific constant shifts estimated from modal allele differences among datasets. The Russian dataset was used as the primary reference alignment because it represented the main study region, provided broad population coverage, and produced a conservative alignment of allele-size distributions. To evaluate the robustness of this choice, additional sensitivity analyses were performed using Alaska and Canada as alternative reference datasets. The resulting harmonized dataset was used for downstream population genetic analyses presented in the associated manuscript. The final aligned dataset includes 1,544 individuals from 42 populations distributed across three major geographic regions of the circumpolar range of Rangifer tarandus. Genotypes are provided for nine microsatellite loci, each represented by two allele columns corresponding to diploid genotypes. The loci included in the dataset are: RT1, RT6, RT7, RT9, RT24, OHEQ, FCB193, BMS745, and BMS1788. Allele sizes are reported as fragment lengths in base pairs after harmonization of dataset-specific allele-size shifts. Validation and sensitivity analyses This updated repository also includes validation and sensitivity statistics documenting the effect of the harmonization procedure on population genetic summary statistics and assessing the robustness of the results to key methodological assumptions. The additional validation materials include: Modal allele shift tables for each locus and dataset. Diversity statistics before and after harmonization, including observed heterozygosity (Ho), expected heterozygosity (He), allelic richness (Ar), and FIS. Sanity-check summaries showing that Ho, He, Ar, and FIS remain unchanged after harmonization. Multi-reference comparison using Russia, Alaska, and Canada as alternative reference datasets. Sensitivity analysis excluding populations with fewer than 20 individuals. Sensitivity analysis excluding loci with large modal allele shifts, using a threshold of ≥40 bp. R script and session information used to reproduce the validation statistics. The invariance of Ho, He, Ar, and FIS after harmonization is mathematically expected because the procedure applies constant locus-specific allele-size shifts within each dataset. This operation changes allele labels but preserves allele frequencies, the number of allelic classes, and the homozygous/heterozygous status of genotypes. Therefore, these analyses should be interpreted as a sanity check confirming that harmonization does not distort within-population diversity estimates. They do not, by themselves, prove that all allele-size differences are purely technical or that the true biological signal was fully recovered. The harmonization procedure should therefore be interpreted as a practical approach for integrating legacy microsatellite datasets when repeated genotyping of shared reference samples is not available. It does not replace cross-laboratory calibration using shared reference samples, which remains the preferred approach when feasible. Access to the files is temporarily restricted while the associated manuscript is under peer review. Access may be granted upon reasonable request for editorial or review purposes. The files are planned to be made openly available after acceptance or publication of the associated manuscript. Data sources The harmonized dataset integrates microsatellite data from several previously published studies: Colson K.E., Mager K.H., Hundertmark K.J. Reindeer introgression and the population genetics of caribou in southwestern Alaska. Journal of Heredity. 2014;105(5):585–596. DOI: 10.1093/jhered/esu030. Serrouya R., Paetkau D., McLellan B.N., Boutin S., Campbell M., Jenkins D.A. Population size and major valleys explain microsatellite variation better than taxonomic units for caribou in western Canada. Molecular Ecology. 2012;21(11):2588–2601. DOI: 10.1111/j.1365-294X.2012.05570.x. Weckworth B.V., Musiani M., McDevitt A.D., Hebblewhite M., Mariani S. Reconstruction of caribou evolutionary history in western North America and its implications for conservation. Molecular Ecology. 2012;21(14):3610–3624. DOI: 10.1111/j.1365-294X.2012.05621.x. Svishcheva G., Babayan O., Sipko T., Kashtanov S., Kholodova M., Stolpovsky Y. Genetic differentiation between coexisting wild and domestic reindeer (Rangifer tarandus L. 1758) in Northern Eurasia. GenResJ. 2022;3:1–14.