Outlier Loci Detect Intraspecific Biodiversity amongst Spring and Autumn Spawning Herring across Local Scales

Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics

The world's oceans are currently facing major stressors in the form of overexploitation and anthropogenic climate change. The Baltic Sea was home to the first "industrial" fishery ∼800 y ago targeting the Baltic herring, a species that is still economically and culturally important today. Yet, the early origins of marine industries and the long-term ecological consequences of historical and contemporary fisheries remain debated. Here, we study long-term population dynamics of Baltic herring to evaluate the past impacts of humans on the marine environment. We combine modern whole-genome data with ancient DNA (aDNA) to identify the earliest-known long-distance herring trade in the region, illustrating that extensive fish trade began during the Viking Age. We further resolve population structure within the Baltic and observe demographic independence for four local herring stocks over at least 200 generations. It has been suggested that overfishing at Øresund in the 16th century resulted in a demographic shift from autumn-spawning to spring-spawning herring dominance in the Baltic. We show that while the Øresund fishery had a negative impact on the western Baltic herring stock, the demographic shift to spring-spawning dominance did not occur until the 20th century. Instead, demographic reconstructions reveal population trajectories consistent with expected impacts of environmental change and historical reports on shifting fishing targets over time. This study illustrates the joint impact of climate change and human exploitation on marine species as well as the role historical ecology can play in conservation and management policies.

A baseline for the genetic stock identification of Atlantic herring, Clupea harengus, in ICES Divisions 6.a, 7.b-c

Atlantic herring in International Council for Exploration of the Sea (ICES) Divisions 6.a, 7.b-c comprises at least three populations, distinguished by temporal and spatial differences in spawning, which have until recently been managed as two stocks defined by geographical delineators. Outside of spawning the populations form mixed aggregations, which are the subject of acoustic surveys. The inability to distinguish the populations has prevented the development of separate survey indices and separate stock assessments. A panel of 45 single-nucleotide polymorphisms, derived from whole-genome sequencing, were used to genotype 3480 baseline spawning samples (2014-2021). A temporally stable baseline comprising 2316 herring from populations known to inhabit Division 6.a was used to develop a genetic assignment method, with a self-assignment accuracy greater than 90%. The long-term temporal stability of the assignment model was validated by assigning archive (2003-2004) baseline samples (270 individuals) with a high level of accuracy. Assignment of non-baseline samples (1514 individuals) from Divisions 6.a, 7.b-c indicated previously unrecognized levels of mixing of populations outside of the spawning season. The genetic markers and assignment models presented constitute a 'toolbox' that can be used for the assignment of herring caught in mixed survey and commercial catches in Division 6.a into their population of origin with a high level of accuracy.

Atlantic herring (Clupea harengus) population structure in the Northeast Atlantic Ocean

The Atlantic herring Clupea harengus L has a vast geographical distribution and a complex population structure with a few very large migratory units and many small local populations. Each population has its own spawning ground and/or time, thereby maintaining their genetic integrity. Several herring populations migrate between common feeding grounds and over-wintering areas resulting in frequent mixing of populations. Thus, many herring fisheries are based on mixed populations of different demographic status. In order to avoid over-exploitation of weak populations and to conserve biodiversity, understanding the population structure and population mixing is important for maintaining biologically sustainable herring fisheries. The aim of this study was to investigate the genetic population structure of herring in the Faroese and surrounding waters, and to develop genetic markers for distinguishing between four herring management units (often called stocks), namely the Norwegian spring-spawning herring (NSSH), Icelandic summer-spawning herring (ISSH), North Sea autumn-spawning herring (NSAH), and Faroese autumn-spawning herring (FASH). Herring from the four stocks were sequenced at low coverage, and single nucleotide polymorphisms (SNPs) were called and used for population structure analysis and individual assignment. An ancestry-informative SNP panel with 118 SNPs was developed and tested on 240 individuals. The results showed that all four stocks appeared to be genetically differentiated populations, but at lower levels of differentiation between FASH and ISSH than the other two populations. Overall assignment rate with the SNP panel was 80.7%, and agreement between the genetic and traditional visual assignment was 75.5%. The NSAH and NSSH samples had the highest assignment rate (100% and 98.3%, respectively) and highest agreement between traditional and genetic assignment methods (96.6% and 94.9%, respectively). The FASH and ISSH samples had substantially lower assignment rates (72.9% and 51.7%, respectively) and agreement between traditional and genetic methods (39.5% and 48.4%, respectively).

Spatial gradients of introgressed ancestry reveal cryptic connectivity patterns in a high gene flow marine fish

Assessing genetic connectivity among populations in high gene flow species is sometimes insufficient to evaluate demographic connectivity. Genetic differentiation quickly becomes zero as soon as a few dozen migrants are exchanged per generation. This provides little information to determine whether migration can ensure demographic coupling. The resulting difficulties in delineating conservation units for the management of commercially exploited marine fish species are well illustrated in the case of the European sea bass (Dicentrarchus labrax). Previous attempts to assess connectivity patterns in the northeast Atlantic have been hampered by a lack of spatial genetic structure. In contrast, mark-recapture data suggested low migration rates between regional spawning areas. Here, we show how a spatial gradient of introgressed Mediterranean ancestry across the northeast Atlantic reflects cryptic patterns of genetic and demographic connectivity. Using a 1K SNP chip data set in 827 individuals sampled from Portugal to the North Sea, we found null overall genetic differentiation across the northeast Atlantic. We however detected a subtle latitudinal admixture gradient originating at the edge of the contact zone with the Mediterranean sea bass lineage. Two significant breaks in the ancestry gradient at the tip of Galicia and northern Brittany indicated barriers to effective dispersal between demographically distinct units. Moreover, a northward expansion signal in Irish and North Seas was revealed by the surfing of rare Mediterranean alleles at the edge of the species range. Our results show that introgressed ancestry gradients offer a powerful alternative to assess genetic and demographic connectivity when the neutral migration-drift balance is not informative.

SNP genotyping reveals substructuring in weakly differentiated populations of Atlantic cod (Gadus morhua) from diverse environments in the Baltic Sea

Atlantic cod (Gadus morhua) is one of the most important fish species in northern Europe for several reasons including its predator status in marine ecosystems, its historical role in fisheries, its potential in aquaculture and its strong public profile. However, due to over-exploitation in the North Atlantic and changes in the ecosystem, many cod populations have been reduced in size and genetic diversity. Cod populations in the Baltic Proper, Kattegat and North Sea have been analyzed using a species specific single nucleotide polymorphism (SNP) array. Using a subset of 8,706 SNPs, moderate genetic differences were found between subdivisions in three traditionally delineated cod management stocks: Kattegat, western and eastern Baltic. However, an FST measure of population differentiation based on allele frequencies from 588 outlier loci for 2 population groups, one including 5 western and the other 4 eastern Baltic populations, indicated high genetic differentiation. In this paper, differentiation has been demonstrated not only between, but also within western and eastern Baltic cod stocks for the first time, with salinity appearing to be the most important environmental factor influencing the maintenance of cod population divergence between the western and eastern Baltic Sea.

Insights into the neutral and adaptive processes shaping the spatial distribution of genomic variation in the economically important Moroccan locust (Dociostaurus maroccanus)

Understanding the processes that shape neutral and adaptive genomic variation is a fundamental step to determine the demographic and evolutionary dynamics of pest species. Here, we use genomic data obtained via restriction site-associated DNA sequencing to investigate the genetic structure of Moroccan locust (Dociostaurus maroccanus) populations from the westernmost portion of the species distribution (Iberian Peninsula and Canary Islands), infer demographic trends, and determine the role of neutral versus selective processes in shaping spatial patterns of genomic variation in this pest species of great economic importance. Our analyses showed that Iberian populations are characterized by high gene flow, whereas the highly isolated Canarian populations have experienced strong genetic drift and loss of genetic diversity. Historical demographic reconstructions revealed that all populations have passed through a substantial genetic bottleneck around the last glacial maximum (~21 ka BP) followed by a sharp demographic expansion at the onset of the Holocene, indicating increased effective population sizes during warm periods as expected from the thermophilic nature of the species. Genome scans and environmental association analyses identified several loci putatively under selection, suggesting that local adaptation processes in certain populations might not be impeded by widespread gene flow. Finally, all analyses showed few differences between outbreak and nonoutbreak populations. Integrated pest management practices should consider high population connectivity and the potential importance of local adaptation processes on population persistence.

Temporal stability and assignment power of adaptively divergent genomic regions between herring (Clupea harengus) seasonal spawning aggregations

Atlantic herring (Clupea harengus), a vital ecosystem component and target of the largest Northwest Atlantic pelagic fishery, undergo seasonal spawning migrations that result in elusive sympatric population structure. Herring spawn mostly in fall or spring, and genomic differentiation was recently detected between these groups. Here we used a subset of this differentiation, 66 single nucleotide polymorphisms (SNPs) to analyze the temporal dynamics of this local adaptation and the applicability of SNP subsets in stock assessment. We showed remarkable temporal stability of genomic differentiation corresponding to spawning season, between samples taken a decade apart (2005 N = 90 vs. 2014 N = 71) in the Gulf of St. Lawrence, and new evidence of limited interbreeding between spawning components. We also examined an understudied and overexploited herring population in Bras d'Or lake (N = 97); using highly reduced SNP panels (N SNPs > 6), we verified little-known sympatric spawning populations within this unique inland sea. These results describe consistent local adaptation, arising from asynchronous reproduction in a migratory and dynamic marine species. Our research demonstrates the efficiency and precision of SNP-based assessments of sympatric subpopulations; and indeed, this temporally stable local adaptation underlines the importance of such fine-scale management practices.