Propose a study design to test whether Eda allele frequency correlates with plate number across marine and freshwater populations.

• A. Collect individuals from both habitats, genotype the Eda locus, measure plate number, perform association tests while controlling for population structure; optionally include a cross to test causality.
• B. Compare only marine populations
• C. Sequence the whole genome and infer plates indirectly
• D. Use observational data from a single lake

Answer: (A)

To test whether Eda allele frequency correlates with plate number across marine and freshwater sticklebacks, collect individuals from multiple marine and freshwater populations, measure their plate number, and determine their Eda genotype. Then analyze whether the Eda genotype explains variation in plate number across these individuals while accounting for population structure. This means using a statistical approach that includes population or ancestry as a covariate or uses a mixed model with a kinship matrix, so you’re separating true genotype–phenotype associations from differences due to shared ancestry or ecotype background.

Including a cross between marine and freshwater lines to test causality can strengthen the evidence, because it examines whether the Eda allele directly influences plate number in a controlled genetic background.

Why other designs aren’t as effective: focusing only on marine populations removes the comparative aspect across habitats; whole-genome sequencing with indirect plate inference is less direct and efficient for answering the specific genotype–plate relationship; sampling from a single lake gives limited variation and little power to separate genetic effects from local environmental factors.

In short, this design directly links Eda genotype to plate variation across ecotypes while controlling for population structure, with a possible cross to probe causality.