Seasonal dynamics of Atlantic herring (Clupea harengus L.) populations spawning in the vicinity of marginal habitats

Genetic Stock Identification Reveals Mismatches Between Management Areas and Population Genetic Structure in a Migratory Pelagic Fish

Sustainable fisheries management is important for the continued harvest of the world's marine resources, especially as they are increasingly challenged by a range of climatic and anthropogenic factors. One of the pillars of sustainable fisheries management is the accurate identification of the biological units, i.e., populations. Here, we developed and implemented a genetic baseline for Atlantic herring harvested in the Norwegian offshore fisheries to investigate the validity of the current management boundaries. This was achieved by genotyping > 15,000 herring from the northern European seas, including samples of all the known populations in the region, with a panel of population-informative SNPs mined from existing genomic resources. The final genetic baseline consisted of ~1000 herring from 12 genetically distinct populations. We thereafter used the baseline to investigate mixed catches from the North and Norwegian Seas, revealing that each management area consisted of multiple populations, as previously suspected. However, substantial numbers (up to 50% or more within a sample) of herring were found outside of their expected management areas, e.g., North Sea autumn-spawning herring north of 62° N (average = 19.2%), Norwegian spring-spawning herring south of 62° N (average = 13.5%), and western Baltic spring-spawning herring outside their assumed distribution area in the North Sea (average = 20.0%). Based upon these extensive observations, we conclude that the assessment and management areas currently in place for herring in this region need adjustments to reflect the populations present. Furthermore, we suggest that for migratory species, such as herring, a paradigm shift from using static geographic stock boundaries towards spatial dynamic boundaries is needed to meet the requirements of future sustainable management regimes.

Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring

The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA, which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB, a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors.

Genetic response to human-induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet, Norway

Habitat changes represent one of the five most pervasive threats to biodiversity. However, anthropogenic activities also have the capacity to create novel niche spaces to which species respond differently. In 1880, one such habitat alterations occurred in Landvikvannet, a freshwater lake on the Norwegian coast of Skagerrak, which became brackish after being artificially connected to the sea. This lake is now home to the European sprat, a pelagic marine fish that managed to develop a self-recruiting population in barely few decades. Landvikvannet sprat proved to be genetically isolated from the three main populations described for this species; that is, Norwegian fjords, Baltic Sea, and the combination of North Sea, Kattegat, and Skagerrak. This distinctness was depicted by an accuracy self-assignment of 89% and a highly significant F ST between the lake sprat and each of the remaining samples (average of ≈0.105). The correlation between genetic and environmental variation indicated that salinity could be an important environmental driver of selection (3.3% of the 91 SNPs showed strong associations). Likewise, Isolation by Environment was detected for salinity, although not for temperature, in samples not adhering to an Isolation by Distance pattern. Neighbor-joining tree analysis suggested that the source of the lake sprat is in the Norwegian fjords, rather than in the Baltic Sea despite a similar salinity profile. Strongly drifted allele frequencies and lower genetic diversity in Landvikvannet compared with the Norwegian fjords concur with a founder effect potentially associated with local adaptation to low salinity. Genetic differentiation (F ST) between marine and brackish sprat is larger in the comparison Norway-Landvikvannet than in Norway-Baltic, which suggests that the observed divergence was achieved in Landvikvannet in some 65 generations, that is, 132 years, rather than gradually over thousands of years (the age of the Baltic Sea), thus highlighting the pace at which human-driven evolution can happen.

Ecological adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci

Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here, we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in herring deviates from expectation under a classical infinitesimal model for complex traits because of large shifts in allele frequencies at hundreds of loci under selection.

Implication of single year seasonal sampling to genetic diversity fluctuation that coordinates with oceanographic dynamics in torpedo scads near Taiwan

Many fisheries management and conservation plans are based on the genetic structure of organisms in pelagic ecosystems; however, these structures tend to vary over time, particularly in cyclic ocean currents. We performed genetic analyses on the populations of the pelagic fish, Megalaspis cordyla (Osteichthyes: Carangidae) in the area surrounding Taiwan during 2000–2001. Genotyping was performed on M. cordyla collected seasonally around Taiwan as well as specimens collected from Singapore (Malacca strait) and Indonesia (Banda Sea). Gonadosomatic indices (GSI) revealed that M. cordyla does not spawn near Taiwan. Data related to the mitochondrial control region revealed that the samples from Singapore and Indonesia represented two distinct genetic cohorts. Genotyping revealed that during the summer (June–August 2000), the Indonesian variant was dominant in eastern Taiwan (presumably following the Kuroshio Current) and in the Penghu region (following the Kuroshio Branch Current). During the same period, the Singapore genotype was dominant along the western coast of Taiwan (presumably following the South China Sea Current); however, the number dropped during the winter (December–February 2001) under the effects of the China Coast Current. Divergence time estimates indicate that the two genetic cohorts split during the last glacial maximum. Despite the fact that these results are based on sampling from a single year, they demonstrate the importance of seasonal sampling in unravelling the genetic diversity in pelagic ecosystems.

Comparative biology and population mixing among local, coastal and offshore Atlantic herring (Clupea harengus) in the North Sea, Skagerrak, Kattegat and western Baltic

The population structure of Atlantic herring (Clupea harengus) from 13 local, coastal and offshore areas of the North Sea, Skagerrak, Kattegat and western Baltic (northeast Atlantic) was studied using biological and environmental data from 1970–2015. The objective was to identify distinct populations by comparing variability in the temporal and spatial phenotypic characteristics and evaluate the potential for mixing of populations in time and space. The populations varied in biological characteristics such as mean vertebral counts (VS), growth and maturity ogives. Generalized additive models indicated temporally stable VS in the North Sea and western Baltic, whereas intra-annual temporal variation of VS occurred in other areas. High variability of VS within a population was not affected by environmental factors such as temperature and salinity. Consequently, seasonal VS variability can be explained by the presence or absence of herring populations as they migrate between areas. The three main populations identified in this paper correspond to the three managed stocks in this area: Norwegian spring spawners (NSS), western Baltic spring spawners (WBSS) and North Sea autumn spawners (NSAS). In addition, several local populations were identified in fjords or lakes along the coast, but our analyses could not detect direct mixing of local populations with the three main populations. Our results highlight the importance of recognizing herring dynamics and understanding the mixing of populations as a challenge for management of herring.

Latitudinal Gradient in Otolith Shape among Local Populations of Atlantic Herring (Clupea harengus L.) in Norway

Otolith shape analysis of Atlantic herring (Clupea harengus) in Norwegian waters shows significant differentiation among fjords and a latitudinal gradient along the coast where neighbouring populations are more similar to each other than to those sampled at larger distances. The otolith shape was obtained using quantitative shape analysis, the outlines were transformed with Wavelet and analysed with multivariate methods. The observed morphological differences are likely to reflect environmental differences but indicate low dispersal among the local herring populations. Otolith shape variation suggests also limited exchange between the local populations and their oceanic counterparts, which could be due to differences in spawning behaviour. Herring from the most northerly location (69°N) in Balsfjord, which is genetically more similar to Pacific herring (Clupea pallasii), differed in otolith shape from all the other populations. Our results suggest that the semi-enclosed systems, where the local populations live and breed, are efficient barriers for dispersal. Otolith shape can thus serve as a marker to identify the origin of herring along the coast of Norway.

Otolith shape: a population marker for Atlantic herring Clupea harengus

Otolith shape variation of seven Atlantic herring Clupea harengus populations from Canada, the Faroe Islands, Iceland, Ireland, Norway and Scotland, U.K., covering a large area of the species' distribution, was studied in order to see if otolith shape can be used to discriminate between populations. The otolith shape was obtained using quantitative shape analysis, transformed with Wavelet and analysed with multivariate methods. Significant differences were detected among the seven populations, which could be traced to three morphological structures in the otoliths. The differentiation in otolith shape between populations was not only correlated with their spawning time, indicating a strong environmental effect, but could also be due to differing life-history strategies. A model based on the shape differences discriminates with 94% accuracy between Icelandic summer spawners and Norwegian spring spawners, which are known to mix at feeding grounds. This study shows that otolith shape could become an accurate marker for C. harengus population discrimination.