Estimating the contribution of Greenland Halibut (Reinhardtius hippoglossoides) stocks to nurseries by means of genotyping-by-sequencing: Sex and time matter

Abstract

Identification of stocks and quantification of their relative contribution to recruitment are major objectives toward improving the management and conservation of marine exploited species. Next-generation sequencing allows for thousands of genomic markers to be analyzed, which provides the resolution needed to address these questions in marine species with weakly differentiated populations. Greenland Halibut (Reinhardtius hippoglossoides) is one of the most important exploited demersal species throughout the North Atlantic, in particular in the Gulf of St. Lawrence, Canada. There, two nurseries are known, the St. Lawrence Estuary and the northern Anticosti Island, but their contribution to the renewal of stocks remains unknown. The goals of this study were (a) to document the genetic structure and (b) to estimate the contribution of the different identified breeding stocks to nurseries. We sampled 100 juveniles per nursery and 50 adults from seven sites ranging from Saguenay Fjord to offshore Newfoundland, with some sites sampled over two consecutive years in order to evaluate the temporal stability of the contribution. Our results show that after removing sex-linked markers, the Estuary/Gulf of St. Lawrence represents a single stock which is genetically distinct from the Atlantic around Newfoundland (F _ST = 0.00146, p-value = .001). Population assignment showed that recruitment in both nurseries is predominantly associated with the St. Lawrence stock. However, we found that the relative contribution of both stocks to the nurseries is temporally variable with 1% contribution of the Newfoundland stock one year but up to 33% for the second year, which may be caused by year-to-year variation in larval transport into the Gulf of St. Lawrence. This study serves as a model for the identification of stocks for fisheries resources in a context where few barriers to dispersal occur, in addition to demonstrating the importance of considering sex-linked markers and temporal replicates in studies of population genomics.

Keywords: Greenland Halibut; management; marine genomics; population assignment; stock identification; temporal stability.

FIGURE 1

Map of sampling sites in Saguenay Fjord (SAGU), St. Lawrence Estuary (ESTU, ESTJ), Gaspé (GASP), North Anticosti Island (NANT, ANTJ), Esquiman (ESQU), and Atlantic Ocean (NFLD, NFLG). The Estuary and northern Anticosti Island nurseries (ESTJ and ANTJ) are defined by the triangles and adult populations of the St. Lawrence and Atlantic (SAGU, NFLD, ESTU, NANT, GASP, and ESQU) by circles. Sites that were sampled for a single year are colored in pink for the first year of sampling and in blue for the second. Those sampled for the two consecutive years are colored in green

FIGURE 2

Population structure for Greenland Halibut from the Estuary/Gulf of St. Lawrence (Saguenay Fjord SAGU, St. Lawrence Estuary ESTU, St. Lawrence Estuary nursery ESTJ, Gaspé GASP, North Anticosti Island NANT, North Anticosti Island nursery ANTJ, and Esquiman ESQU) and Newfoundland (NFLD and NFLG) using ADMIXTURE: (a) for dataset including sex‐linked markers and (b) for dataset without sex‐linked markers. Results are shown for K = 2. Sites are classified from west to east and individuals in alphanumerical order. Sites sampled for two consecutive years are combined

FIGURE 3

Boxplot of q‐values separated by sex when performing ADMIXTURE using the dataset with sex‐linked markers

FIGURE 4

Principal component analysis (PCA) using (a) and (b) dataset including sex‐linked markers and (c) and (d) the dataset without sex‐linked markers. Females are colored in pink and males in blue in (a) and (c) and individuals are colored by population in (b) and (d)

FIGURE 5

Monte Carlo cross‐validation test for SNPs dataset using different proportions of training loci (0.1, 0.25, 0.5, 0.75, and 1) and individuals in training sets. Boxplots were generated for overall sources populations (left) and for both populations separately (GSL in center and NFL to the right). Selected SNPs were ranked in decreasing values of differentiation index when using a different proportion then 1

FIGURE 6

Individual assignment test (a) for the first year of sampling and (b) for the second year of sampling to reference stocks of Gulf of St. Lawrence (GSL) and Newfoundland (NFL). All loci and individuals were kept for the test