RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity

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 abi...

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Bibliographic Details
Published in:	Royal Society open science Vol. 4; no. 2; p. 160548
Main Authors:	Vendrami, David L. J., Telesca, Luca, Weigand, Hannah, Weiss, Martina, Fawcett, Katie, Lehman, Katrin, Clark, M. S., Leese, Florian, McMinn, Carrie, Moore, Heather, Hoffman, Joseph I.
Format:	Journal Article
Language:	English
Published:	England The Royal Society Publishing 01-02-2017 The Royal Society
Subjects:	Genetics Great Scallop Microsatellite Morphometrics pecten maximus Phenotypic Plasticity Single Nucleotide Polymorphism Pecten maximus great scallop microsatellite phenotypic plasticity single nucleotide polymorphism morphometrics
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Summary:	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 population structure and phenotypic plasticity in natural populations.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors contributed equally to this study. Electronic supplementary material is available online at https://dx.doi.org/10.6084/m9.figshare.c.3672256.
ISSN:	2054-5703 2054-5703
DOI:	10.1098/rsos.160548