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Supplementary figure 7: Results of the Structure analysis after having excluded samples collected from Mulroy Bay. Results are shown for 13 microsatellites (panels a and b) and 10,539 SNPs (panels c and d). Panels (a) and (c) show mean +/- SE Ln P(D) values of five replicate Structure runs for each value of K, the hypothesised number of clusters in the data, ranging from one to nine. Panels (b) and (d) show the resulting cluster membership coefficients of each individual

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posted on 04.02.2017, 07:13 by David L. J. Vendrami, Luca Telesca, Hannah Weigand, Martina Weiss, Katie Fawcett, Katrin Lehman, M. S. Clark, Florian Leese, Carrie McMinn, Heather Moore, Joseph I. Hoffman
The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops (Pecten maximus) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher Fst values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying both population structure and phenotypic plasticity in natural populations.