Context

The NSFB18W2 population shows:

  • High heterozygosity
  • Low Fis
  • Moderate LD-based Ne (1,716–1,880)

All of these metrics were calculated from the same genotype dataset, yet seem to suggest slightly different population histories. At first glance, high heterozygosity and low Fis might suggest a larger Ne, so why is the LD-based Ne only moderate?

Key Points

1. LD-based Ne is Sensitive to Short-Term Demography

  • LD Ne reflects recent (1–3 generation) effective size, based on non-random associations between loci (linkage disequilibrium).
  • It’s especially sensitive to rare allele frequencies and recent bottlenecks or structure.
  • LD can remain high after a recent bottleneck, even if heterozygosity remains high.

2. Heterozygosity and Fis Reflect Broader Patterns

  • Heterozygosity (H) measures allelic diversity and is shaped over longer timescales.
  • Fis reflects inbreeding and is often close to zero when mating is random or outcrossed.
  • These metrics are less sensitive to rare alleles or recent stochastic changes.

3. Gene Flow and Admixture Effects

  • If NSFB18W2 has recent gene flow or admixture, this:
    • Increases heterozygosity,
    • Decreases Fis (heterozygote excess),
    • But can inflate LD, reducing LD Ne estimates.

4. Substructure Can Confound LD Ne

  • The Wahlund effect or hidden substructure:
    • May artificially lower LD Ne,
    • Even while maintaining high H and low Fis.

5. Shared Data ≠ Identical Signal

  • Even when computed from the same dataset, these statistics:
    • Focus on different dimensions of genetic variation,
    • Respond to different demographic events,
    • And can appear mildly discordant without being contradictory.

Conclusion

NSFB18W2’s combination of high heterozygosity, low Fis, and moderate LD-based Ne is not surprising or contradictory. These metrics capture different aspects of genetic and demographic history—even when drawn from the same dataset.

The moderate Ne estimate may reflect recent demographic constraints, fine-scale structure, or elevated LD from historical factors, while the high heterozygosity and low Fis reflect a well-mixed, diverse gene pool.