Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in...

Area of Science:

• * Population Genetics
• * Molecular Ecology
• * Marine Biology

Background:

• * Phylogeographic studies rely on robust genomic sampling for accurate gene flow inferences.
• * Amplified Fragment Length Polymorphisms (AFLPs) offer a cost-effective method for generating multilocus allele frequency data.
• * The balance between minimizing genotyping error and retaining sufficient genetic markers in AFLP analysis requires empirical evaluation.

Purpose of the Study:

• * To evaluate the tradeoff between reducing genotyping error and preserving population genetic signal in AFLP data.
• * To compare population structure and gene flow in two co-distributed oyster species: broadcast spawning (Crassostrea virginica) and brooding (Ostrea equestris).
• * To develop a general method for empirically assessing these tradeoffs in AFLP studies.

Main Methods:

• * Utilized Amplified Fragment Length Polymorphisms (AFLPs) for population genetic analysis.
• * Employed automated marker selection and scoring methods.
• * Compared population structure across datasets with varying mean mismatch error rates (0% to >4%) to identify optimal data subsets.

Main Results:

• * Artifactual population structure was detected in datasets with high average mismatch error rates (≥2% and >4%).
• * Crucial population substructure signals were lost when error rates were excessively minimized.
• * The brooding oyster (Ostrea equestris) exhibited higher gene flow compared to the broadcast spawner (Crassostrea virginica).

Conclusions:

• * Overly stringent culling of loci based on genotyping error can lead to a loss of biologically relevant population genetic information.
• * Empirical evaluation of error rate tradeoffs is crucial for reliable phylogeographic inferences using AFLPs.
• * The findings provide a methodological framework for optimizing AFLP data analysis in population genetics research.