Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation

Carlos Carreras,Lorenzo Zane,Enrique Macpherson,Claudia Kruschel,Marta Pascual,Víctor Ordóñez,Ina Nasto

doi:10.1038/srep43417

Abstract

The assessment of the genetic structuring of biodiversity is crucial for management and conservation. For species with large effective population sizes a low number of markers may fail to identify population structure. A solution of this shortcoming can be high-throughput sequencing that allows genotyping thousands of markers on a genome-wide approach while facilitating the detection of genetic structuring shaped by selection. We used Genotyping-by-Sequencing (GBS) on 176 individuals of the endemic East Atlantic peacock wrasse (Symphodus tinca), from 6 locations in the Adriatic and Ionian seas. We obtained a total of 4,155 polymorphic SNPs and we observed two strong barriers to gene flow. The first one differentiated Tremiti Islands, in the northwest, from all the other locations while the second one separated east and south-west localities. Outlier SNPs potentially under positive selection and neutral SNPs both showed similar patterns of structuring, although finer scale differentiation was unveiled with outlier loci. Our results reflect the complexity of population genetic structure and demonstrate that both habitat fragmentation and positive selection are on play. This complexity should be considered in biodiversity assessments of different taxa, including non-model yet ecologically relevant organisms.

Highlights

The assessment of marine biodiversity, including genetic structuring, is one of the major goals of population management and conservation biology[1]
In this study we used GBS to study the genetic structure of an ecologically relevant Mediterranean endemic fish, for which traditional markers had revealed a genetic structuring not consistent with the known biology of the species, showing how these new genomic approaches could change our vision of marine molecular ecology and evolution
Using 8 microsatellites, Galarza et al.[3] found significant genetic structuring in Symphodus tinca populations only along the Almeria-Oran Front, an oceanographic discontinuity in the west Mediterranean that has been reported to be a barrier to gene flow for a high number of species[39]

Summary

Introduction

The assessment of marine biodiversity, including genetic structuring, is one of the major goals of population management and conservation biology[1]. The East Atlantic peacock wrasse (Symphodus tinca, Linnaeus, 1758) has several biological features that make this non-model organism a good candidate to study genetic structuring caused by both isolation and local adaptation This demersal fish is considered a key species due to its abundance and generalist diet (sea-urchins, ophiuroids, bivalves, shrimps and crabs), being an important prey of large predators[29], as well as constituting a common species in artisanal and spear fishing activities[30]. The species lives mainly in shallow rocky shores with a high abundance of arborescent algae to build the nests[33], which is common in the sampled localities of the Adriatic Sea Pilot Study[35] Considering all these biological characteristics it is expected that the East Atlantic peacock wrasse would have a very limited dispersion range generating strong genetic population differentiation.

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Conclusion