Integrating microsatellite data via locus-specific mode-shift harmonisation reveals circumpolar population structure in reindeer and caribou (Rangifer tarandus).

Reindeer and caribou (Rangifer tarandus) occupy a vast northern range spanning Eurasia and North America, where understanding population structure is essential for conservation and management. However, comparative analyses across this circumpolar distribution are hindered by systematic allele-size offsets introduced by differences in genotyping platforms, laboratory protocols, and allele-calling procedures. Here, we applied a locus-specific mode-shift harmonisation procedure to integrate legacy microsatellite datasets from Alaska, Canada, and Russia. The final harmonised dataset included 1544 individuals from 42 populations genotyped at nine shared microsatellite loci. The procedure used dataset- and locus-specific modal allele differences to reduce systematic allele-size offsets while preserving within-dataset allele-frequency structure and heterozygosity status. To evaluate robustness, we compared diversity statistics before and after harmonisation, tested alternative reference alignments, and performed sensitivity analyses excluding populations with small sample sizes and loci with large modal allele shifts. We also assessed a pooled small-sample dataset in which sparsely represented populations were grouped within biologically meaningful regional or ecological units. Diversity estimates remained unchanged after harmonisation, as expected for constant locus-specific allele-size shifts, and broad interregional structure was retained across reference alignments and sensitivity filters. After harmonisation, PCA, DAPC, Nei-distance analysis, pairwise FST, and exploratory ADMIXTURE analyses consistently supported broad differentiation among Russian, Canadian, and Alaskan populations, with Alaskan populations occupying an intermediate position between Canadian and Russian groups. These results are consistent with historical connectivity across the Beringian region. Our study shows that reference-based mode-shift harmonisation can provide a practical framework for improving the comparability of heterogeneous microsatellite datasets when shared reference samples are unavailable, while remaining complementary to direct cross-laboratory calibration approaches.