title: RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity.
abstract: 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 higherFstvalues 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.
authors.affiliation: Department of Animal Behavior , University of Bielefeld , Postfach 100131, 33501 Bielefeld , Germany.
authors.forename: David L J
authors.identifier: 0000-0001-9409-4084
authors.initials: DL
authors.lastname: Vendrami
authors.affiliation: Department of Earth Sciences , University of Cambridge , Downing Street, Cambridge, Cambridgeshire, CB2 3EQ , UK.
authors.forename: Luca
authors.identifier: 0000-0002-9060-2261
authors.initials: L
authors.lastname: Telesca
authors.affiliation: Faculty of Biology, Aquatic Ecosystem Research , University of Duisburg-Essen , Universitaetsstrasse 5, 45141 Essen , Germany.
authors.forename: Hannah
authors.initials: H
authors.lastname: Weigand
authors.affiliation: Faculty of Biology, Aquatic Ecosystem Research , University of Duisburg-Essen , Universitaetsstrasse 5, 45141 Essen , Germany.
authors.forename: Martina
authors.initials: M
authors.lastname: Weiss
authors.affiliation: Department of Animal Behavior , University of Bielefeld , Postfach 100131, 33501 Bielefeld , Germany.
authors.forename: Katie
authors.initials: K
authors.lastname: Fawcett
authors.affiliation: Department of Animal Behavior , University of Bielefeld , Postfach 100131, 33501 Bielefeld , Germany.
authors.forename: Katrin
authors.initials: K
authors.lastname: Lehman
authors.affiliation: British Antarctic Survey , Natural Environment Research Council , High Cross, Madingley Road, Cambridge CB3 0ET , UK.
authors.forename: M S
authors.initials: MS
authors.lastname: Clark
authors.affiliation: Faculty of Biology, Aquatic Ecosystem Research , University of Duisburg-Essen , Universitaetsstrasse 5, 45141 Essen , Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Leese
authors.affiliation: Agri-Food and Biosciences Institute , Fisheries and Aquatic Ecosystems , 18a Newforge Lane, Belfast BT9 5PX , UK.
authors.forename: Carrie
authors.initials: C
authors.lastname: McMinn
authors.affiliation: Agri-Food and Biosciences Institute , Fisheries and Aquatic Ecosystems , 18a Newforge Lane, Belfast BT9 5PX , UK.
authors.forename: Heather
authors.initials: H
authors.lastname: Moore
authors.affiliation: Department of Animal Behavior , University of Bielefeld , Postfach 100131, 33501 Bielefeld , Germany.
authors.forename: Joseph I
authors.initials: JI
authors.lastname: Hoffman
keywords: Pecten maximus; great scallop; microsatellite; morphometrics; phenotypic plasticity; single nucleotide polymorphism