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

Vendrami, David L. J. and Telesca, Luca and Weigand, Hannah and Weiss, Martina and Fawcett, Katie and Lehman, Katrin and Clark, M. S. and Leese, Florian and McMinn, Carrie and Moore, Heather and Hoffman, Joseph I. (2017) RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity. Royal Society Open Science, 4 (2). p. 160548. ISSN 2054-5703 DOI https://doi.org/10.1098/rsos.160548

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Official URL: https://doi.org/10.1098/rsos.160548


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.

Item Type: Article
Uncontrolled Keywords: 2017AREP; IA76
Subjects: 04 - Palaeobiology
Divisions: 04 - Palaeobiology
07 - Gold Open Access
12 - PhD
Journal or Publication Title: Royal Society Open Science
Volume: 4
Page Range: p. 160548
Identification Number: https://doi.org/10.1098/rsos.160548
Depositing User: Sarah Humbert
Date Deposited: 09 Apr 2020 22:43
Last Modified: 09 Apr 2020 22:43
URI: http://eprints.esc.cam.ac.uk/id/eprint/4667

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