A Parallel Population Genomic and Hydrodynamic Approach to Fishery Management of Highly-Dispersive Marine Invertebrates: The Case of the Fijian Black-Lip Pearl Oyster Pinctada margaritifera.

Monal M Lal,Dean R Jerry,Paul C Southgate,Kyall R Zenger,Cyprien Bosserelle

doi:10.1371/journal.pone.0161390

Abstract

Fishery management and conservation of marine species increasingly relies on genetic data to delineate biologically relevant stock boundaries. Unfortunately for high gene flow species which may display low, but statistically significant population structure, there is no clear consensus on the level of differentiation required to resolve distinct stocks. The use of fine-scale neutral and adaptive variation, considered together with environmental data can offer additional insights to this problem. Genome-wide genetic data (4,123 SNPs), together with an independent hydrodynamic particle dispersal model were used to inform farm and fishery management in the Fijian black-lip pearl oyster Pinctada margaritifera, where comprehensive fishery management is lacking, and the sustainability of exploitation uncertain. Weak fine-scale patterns of population structure were detected, indicative of broad-scale panmixia among wild oysters, while a hatchery-sourced farmed population exhibited a higher degree of genetic divergence (Fst = 0.0850–0.102). This hatchery-produced population had also experienced a bottleneck (NeLD = 5.1; 95% C.I. = [5.1–5.3]); compared to infinite NeLD estimates for all wild oysters. Simulation of larval transport pathways confirmed the existence of broad-scale mixture by surface ocean currents, correlating well with fine-scale patterns of population structuring. Fst outlier tests failed to detect large numbers of loci supportive of selection, with 2–5 directional outlier SNPs identified (average Fst = 0.116). The lack of biologically significant population genetic structure, absence of evidence for local adaptation and larval dispersal simulation, all indicate the existence of a single genetic stock of P. margaritifera in the Fiji Islands. This approach using independent genomic and oceanographic tools has allowed fundamental insights into stock structure in this species, with transferability to other highly-dispersive marine taxa for their conservation and management.

Highlights

Sustainable management and conservation of marine species is faced with a number of challenges, among which is the wide distribution of taxa across diverse habitats and geopolitical jurisdictions, that make species-specific management plans difficult to design and implement
The primary dataset of 42,341 SNPs was screened to retain only the single most informative SNP per locus, remove those loci significantly deviating from Hardy-Weinberg Equilibrium (HWE) (p
By independently evaluating population genomic analyses with hydrodynamic dispersal simulation, we identified that Fijian P. margaritifera display a very shallow pattern of population structure, and are highly likely to constitute a single, biologically significant stock for fishery management

Summary

Introduction

Sustainable management and conservation of marine species is faced with a number of challenges, among which is the wide distribution of taxa across diverse habitats and geopolitical jurisdictions, that make species-specific management plans difficult to design and implement. Reiss et al [3] make the observation that many fishery management and assessment tools focus primarily on the ecological aspects of populations (e.g. population growth and mortality rates), while overall management goals include many evolutionary criteria such as the conservation of genetic diversity and maintenance of sustainable spawning stock biomass. This disconnect highlights the need for bridging the gap between fisheries management and population genetics, and for characterising stock boundaries, identifying the level of divergence required to manage two populations together, or as separate entities [3,4,5,6,7]

Methods

Results

Discussion

Conclusion