Population genomics reveals a mismatch between management and biological units in green abalone (Haliotis fulgens)

Seascape genomics of the pink abalone (Haliotis corrugata): An insight into a cross-border species in the northeast Pacific coast

Seascape genomics gives insight into the geographic and environmental factors shaping local adaptations. It improves the understanding of the potential effects of climate change, which is relevant to provide the basis for the international management of fishery resources. The pink abalone (Haliotis corrugata) is distributed from California, United States to Baja California Sur, Mexico, exposed to a latitudinal environmental gradient in the California Current System. Management of the pink abalone contrasts between Mexico and the United States; Mexico has an active fishery organized in four administrative areas, while the United States has kept the fishery in permanent closure since 1996. However, the impact of environmental factors on genetic variation along the species distribution remains unknown, and understanding this relationship is crucial for effective spatial management strategies. This study aims to investigate the neutral and adaptive genomic structure of H. corrugata. A total of 203 samples from 13 locations were processed using ddRADseq, and covering the species' distribution. Overall, 2,231 neutral, nine potentially adaptive and three genomic-environmental association loci were detected. The neutral structure identified two groups: 1) California, United States and 2) Baja California Peninsula, México. In addition, the adaptive structure analysis also detected two groups with genetic divergence observed at Punta Eugenia. Notably, the seawater temperature significantly correlated with the northern group (temperate) and the southern (warmer) group. This study is a valuable foundation for future research and conservation initiatives, emphasizing the importance of considering neutral and adaptive genetic factors when developing management strategies for marine species.

Short-term effects of community-based marine reserves on green abalone, as revealed by population studies

Marine reserves (MRs) are implemented worldwide to protect, restore, and manage marine ecosystems and species. However, it is important to document the positive effects those marine reserves have on slow-growth, temperate invertebrates such as abalone. Abalone, Haliotis spp., are marine gastropods of high economic value extracted worldwide for decades, which has led to fisheries-driven population decreases. In this work, we focused on a case study and assessed the short-term (1-2 years) effects of marine reserves established and managed by a local fishing cooperative at Guadalupe Island, Mexico. We evaluated the population status of green abalone, H. fulgens, by conducting (1) an assessment of the green abalone population around Guadalupe Island through subtidal monitoring and (2) an evaluation of the effect of two recently established marine reserves on population parameters such as the increase in density (individuals·m2), biomass, number of aggregated abalone, egg production, and proportion of individuals bigger than 150 mm (minimum harvest size) compared to fished areas. To assess the population around Guadalupe Island, we surveyed 11,160 m2 during 2020 and 2021. We recorded 2327 green abalones with a mean ± SE shell length of 135.978 ± 0.83 mm and a mean density of 0.21 ± 0.02 individuals·m2. All variables were statistically higher at the MRs except for shell length in 2021. In this work, we report for the first time the green abalone population status at Guadalupe Island and a positive short-term biological response to community-based marine reserves. This study suggests that a network of MRs combined with good management could help abalone populations in the short term in Guadalupe Island, potentially leading to more sustainable fishing practices and social-ecological resilience.

Coastal upwelling influences population structure of dusky grouper Epinephelus marginatus: An integrative approach based on otolith chemistry and muscle stable isotopes

The dusky grouper (Epinephelus marginatus) is an overfished and threatened fish species with coastal distribution. In the Southwestern Atlantic, it occurs across a broad region influenced by two major oceanographic features: the Cabo Frio (23°S) and the Cabo Santa Marta (28°S) upwelling systems. Along the Brazilian coast, the species may present continuous or discrete populations, depending on the methodological approach used. In this study we combined otolith chemistry and muscle stable isotope analyses to examine the population structure of dusky groupers and its association with the two upwelling systems. Fish were collected in shallow coastal waters of the Southwest Atlantic Ocean, covering the southeastern and southern Brazilian coasts, among Macaé (22°S), Santos (24°S), Florianópolis (27°S), and in Rio Grande (32°S). The results show three statistically well-separated population groups along the region. We named these population groups as North (north of Cabo Frio); Center (between upwelling regions); and South (south of the Cabo Santa Marta system). Our findings allow to suggest that the upwelling systems may influence the distribution of E. marginatus stocks along the Brazilian south-western coast, even though a causal effect may not be attributed at this point. Overall, this combined approach, leveraging information from distinct natural tags, and reflecting variability of water chemistry and food webs with latitude, allowed us to enhance our understanding on how major upwelling systems influence the structuring of fish populations along the southwestern Atlantic Ocean.

Genomic Stock Structure of the Marine Teleost Tarakihi (Nemadactylus macropterus) Provides Evidence of Potential Fine-Scale Adaptation and a Temperature-Associated Cline Amid Panmixia

Tarakihi (Nemadactylus macropterus) is an important fishery species with widespread distribution around New Zealand and off the southern coasts of Australia. However, little is known about whether the populations are locally adapted or genetically structured. To address this, we conducted whole-genome resequencing of 175 tarakihi from around New Zealand and Tasmania (Australia) to obtain a dataset of 7.5 million genome-wide and high-quality single nucleotide polymorphisms (SNPs). Variant filtering, FST-outlier analysis, and redundancy analysis (RDA) were used to evaluate population structure, adaptive structure, and locus-environment associations. A weak but significant level of neutral genetic differentiation was found between tarakihi from New Zealand and Tasmania (FST = 0.0054–0.0073, P ≤ 0.05), supporting the existence of at least two separate reproductive stocks. No clustering was detected among the New Zealand populations (ΦST < 0.001, P = 0.77). Outlier-based, presumably adaptive variation suggests fine-scale adaptive structure between locations around central New Zealand off the east (Wairarapa, Cape Campbell, and Hawke’s Bay) and the west coast (Tasman Bay/Golden Bay and Upper West Coast of South Island). Allele frequencies from 55 loci were associated with at least one of six environmental variables, of which 47 correlated strongly with yearly mean water temperature. Although genes associated with these loci are linked to various functions, the most common functions were integral components of membrane and cilium assembly. Projection of the RDA indicates the existence of a latitudinal temperature cline. Our work provides the first genomic insights supporting panmixia of tarakihi in New Zealand and evidence of a genomic cline that appears to be driven by the temperature gradients, together providing crucial information to inform the stock assessment of this species, and to widen the insights of the ecological drivers of adaptive variation in a marine species.