To provide secondary genetic confirmation of observed stock collapses observed in abundance data and using effective size reconstruction, we also tested for the presence of recent genetic bottlenecks in LG1 homozygous noninverted, heterozygous, and LG1 homozygous inverted groups. We analyzed 6270 genome-wide SNPs excluding LG1 and LG12 rearrangements in each group using the BOTTLENECK (31) software to detect bottlenecks assuming an infinite alleles model. We inferred bottlenecks from presence of a mode shift in allele frequency toward reduction in the number of low frequency alleles or significant sign and standardized differences test results.

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