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 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

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 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

Sustainable management of Mytilus edulis seed resources in Northern Ireland

The bottom mussel industry in Northern Ireland is threatened by a number of issues arising due to overfishing and variable settlement success of mussel seed. Investigations on the Skullmartin mussel seed bed showed ~gative impacts of dredging. However, as Skullmartin is a sink: for mussel larvae, fishing ofthe bed is likely to be sustainable as long as the source ofthe larvae is maintained. The biodiversity of Skullmartin was adversely affected by dredging. Species richness and diversity decreased after dredging. However, these effects were short-lived, with species richness recovering once dredging had ceased. The transport ofstarfish from seed. bed to relaying site is a problem facing all bottom mussel growers. The mostefficient method to reduce the transport of starfish is to submerge the contents ofthe hold with freshwater. This led to 100 % mortality of starfish after 12 hours. Desiccation ofstarfish, which is used in the 1'.Torthern Ireland industry, was found to be inefficient as it required 48 hours to cause 100 % mortality, with . large mussel mortality also occurring after this time. As mussel seed is a limited resource it is imperative that it is managed efficiently. Relaying trials found that although meat content and shell length are adversely affected by an increasing relaying density, it is the marketable yield which is most affected, ,with a density of75 tha-l exceeding the carrying capacity of the study site. Spat collectors, were examined as a sustainable source ofmussel seed. Peaks in settlement appeared in the summer and Belfast Lough was found to have a significantly larger settlement than Carlingford Lough due to the larger coverage of licensed mussel relaying plot in Belfast Lough which can directly attribute to the larval supply in the Lough.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Data from: 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 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

A Global Review of Catch Efficiencies of Towed Fishing Gears Targeting Scallops

Publication history: Published online - 29 October 2022.The catch efficiency of towed fishing gears is the fraction of the target species in the gear path that were caught and retained. Catch efficiency is fundamental for calculating population status required for establishing fisheries management reference points. Consequently, catch efficiency has been estimated for many commercially important scallop (Pectinid) fisheries. This article synthesizes and discusses estimates of catch efficiency of towed gears used to target scallops, the methods for estimating catch efficiency and the factors that influence these estimates. There exists considerable variation in catch efficiency estimates among studies (0.1 to 0.7), and it is important that this variation is accounted for during surveys and stock assessments to avoid erroneous advice and estimates. The high variation was driven by differences in experimental conditions, estimation methods and scallop behavior. Scallop size and substrate type were the two most common reporting categories discussed in the studies and consequently should be considered the two most important drivers of catch efficiency. Other important factors such as gear specifications, and scallop species were featured in some studies. This review will be highly useful for designing catch efficiency experiments, survey design and stock assessments by understanding, and accounting for, catch efficiency variation.This research was not funded by any particular grants. The authors come from a range of institutions and their general research time is funded by a variety of sources including from research councils, charities, fishing industries and governments

Pmaximus_Microsatellite_genotypes

The file contains data for 180 samples of great scallop (Pecten maximus) genotyped at 13 microsatellite loci. These samples where collected from nine locations along the coast of Northern Ireland

Supplementary information 3: Computer code and accompanying documentation for morphometrics and colourimetric analyses from 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 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 (<i>Pecten maximus</i>) 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 <i>F</i>_st 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

Supplementary information 2: Detailed ddRAD library preparation protocol from 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 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 (<i>Pecten maximus</i>) 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 <i>F</i>_st 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

Supplementary figure 1: Illustration of the process of generating scallop shell outline coordinates for the geometric morphometrics analysis. From left to right: scaled digital photograph, isolated shell outline, and 1000 pseudo-landmarks placed along the shell perimeter from 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 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 (<i>Pecten maximus</i>) 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 <i>F</i>_st 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

Supplementary table 2: Pairwise Fst values (below diagonal) and corresponding p-values (above diagonal) calculated using (a) 13 microsatellites genotyped in 180 individuals and (b) 10,539 SNPs genotyped in 45 individuals from 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 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 (<i>Pecten maximus</i>) 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 <i>F</i>_st 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