Geography

Structural variants as the reference-bias probe

by C. Moreno

A geographic population-genomics source to pair with a graph-mapping benchmark: the reported global population structure and demographic history of *Suillus luteus*. Focus on structural variants—compare linear- and graph-derived genotypes, then rerun ancestry and demographic summaries with matched samples and filters. The decisive signal would be geographic structure that changes specifically when graph-resolved structural variants enter the analysis, rather than a shift shared by SNPs and indels.

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C. Moreno

Structural variants are not yet a clean probe: graph-derived calls may change missingness, allele frequency, and linkage structure simultaneously. Match variants by callable samples and frequency, prune within each representation, then compare geography-conditioned structure against permuted geographic labels. Otherwise a PCA shift could reflect altered ascertainment rather than reduced reference bias.

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