The importance of sampling design: spatial patterns and clonality in estimating the genetic diversity of coral reefs

The interpretation of genetic variation on and among corals on reefs has rarely been contextualized in an explicitly spatial framework where each individual has both genetic and spatial parameters. Here, we explore interactions between sampling effort, sampling design, and the presence of spatial genetic structure (SGS) on the ability to effectively characterize genetic diversity on a coral reef. To do this, we take our dataset of 2352 genotypes (78 unique multi-locus genotypes) of the coral, Pocillopora damicornis, collected from June 2007 to October 2009, a dataset of near-exhaustive sampling of a single patch reef in KAne'ohe Bay, Hawai'i (21A degrees 27.462N, 157A degrees 48.405W), and subsample from it using three different strategies: (1) random sampling from throughout the reef; (2) saturation sampling all corals from within a pre-defined area of the reef, avoiding the reef's edge; and (3) sampling all nearest neighbors of a randomly chosen coral while allowing for the inclusion of the reef's edge. Our results demonstrate appreciable variation (e.g., 0.35-0.46) in estimates of observed heterozygosity (H (O)) using a typical sample size of 50 and that in the presence of SGS, non-random sampling schemes can give biased estimates of genetic diversity. Furthermore, our results indicate that over 1000 samples (i.e., similar to 40 % of the total number of colonies) are required to reveal the true pattern of spatial genetic structure at our site. We also demonstrate by rarefaction analysis that the bias in estimating clonal richness (i.e., the proportion of unique genotypes in a given sampling area relative to the total number of samples surveyed) for small sample numbers is due to the predominance of clones (i.e., high level of clonality) and not skew in genet frequency distribution. Overall, we argue that: (1) consideration of sampling design is important in population genetic studies, particularly since non-random sampling in the presence of SGS can give biased estimates of genetic diversity and (2) intense to near-exhaustive sampling schemes may be important for characterizing genetic diversity in highly clonal populations.