Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the NW Mediterranean Sea

Abstract

By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while raising new ones. The latter include how different local environments influence adaptive and neutral genomic variation within and among populations, providing insights into local adaptation of natural populations and their responses to global change. Here, under a seascape genomic approach, ddRAD data of 4609 SNPs from 398 sardines (Sardina pilchardus) collected in 11 Mediterranean and one Atlantic site were generated. These were used along with oceanographic and ecological information to detect signals of adaptive divergence with gene flow across environmental gradients. The studied sardines constitute two clusters (FST=0.07), a pattern attributed to outlier loci, highlighting putative local adaptation. The trend in the number of days with sea surface temperature above 19oC, critical threshold Please note that this is an author-produced PDF of an article accepted for publication following peer review. The definitive publisher-authenticated version is available on the publisher Web site.for successful sardine spawning, was crucial at all levels of population structuring with implications on species' key biological processes. Outliers link candidate SNPs to the region's environmental heterogeneity. Our findings provide evidence for a dynamic equilibrium where population structure is maintained by physical and ecological factors under the opposing influences of migration and selection. This dynamic in nature system, warrants continuous monitoring under a seascape genomic approach that might benefit from a temporal and more detailed spatial dimension. Our results may contribute to complementary studies aimed at providing deeper insights into the mechanistic processes underlying population structuring. Those are key for understanding and predicting future changes and responses of this highly exploited species in the face of climate change.

Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble beeBombus vosnesenskii

“…Li et al, 2017; Manel, Schwartz, Luikart, & Taberlet, 2003). Spatially complex landscapes have features that might constrain gene flow, increasing population genetic structure of inhabitants compared to more homogeneous landscapes (Rahbek et al, 2019; Wang & Singh, 2019) and also harbor substantial abiotic variation that could drive local adaptation in populations from dissimilar environments (Andrews et al, 2022; Antoniou et al, 2023; Capblancq, Fitzpatrick, Bay, Exposito-Alonso, & Keller, 2020; Heraghty, Rahman, Jackson, & Lozier, 2022). Genomic data can be used to understand current and historical population structure as well as genome- environment associations that might signal local adaptation and can thus provide multiple types of information about evolutionary responses to complex landscapes in widespread species.…”

Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii

“…The degree of spatial and environmental heterogeneity across a species range can have important effects on gene flow and population structure (Li et al, 2017; Manel et al, 2003). Spatially complex landscapes have features that might constrain gene flow, increasing population genetic structure of inhabitants compared with more homogeneous landscapes (Rahbek et al, 2019; Wang & Singh, 2019) and also harbour substantial abiotic variation that could drive local adaptation in populations from dissimilar environments (Andrews et al, 2022; Antoniou et al, 2023; Capblancq, Fitzpatrick, et al, 2020; Heraghty et al, 2022). Genomic data can be used to understand current and historical population structure as well as genome–environment associations that might signal local adaptation and can thus provide multiple types of information about evolutionary responses to complex landscapes in widespread species.…”

Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish—Implications for Broodstock Provenance Sourcing and Larval Production

“…Functional annotation analyses of the environment-associated RAD loci revealed that the gene sets linked to these loci play a key role in biological processes associated with environmental pressures. The retrieved top GO categories (e.g., cellular process, developmental process, metabolism, biological regulation, and response to stimulus) have been reported in other studies that measure transcriptomic responses under experimentally induced heat stress [165,166], ocean acidification [167,168], biomineralisation, energy metabolism, and heat, disease, or hypoxia tolerance [40,169]. Moreover, the gene sets reported in the present study were enrichment in four functional pathways, which included the WNT-, MAPK-, RIG-I-like receptor and Hedgehog signalling pathways and Glycerophospholipid metabolism.…”

“…Indeed, the abiotic environment acts as a selective force on natural populations, shaping and maintaining variation in heritable traits (morphology, physiology, and behaviour) that provide significantly greater fitness in their local environment (i.e., local adaptation) when compared to populations from other environments [34][35][36][37]. Understanding the extent and scale of local adaptation is critical in determining how quickly and to what extent specific populations will respond to habitat changes, climate change, fisheries-or farming-induced evolution and interactions with a hatchery-or captive-reared counterparts [36,[38][39][40].…”