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The genomic diversity and population structure of marine species represents a complex mosaic shaped by historical and contemporary environmental seascape features that maintain or alter it over time. The Gulf of California (GC) is an interior sea with a dynamic history during its formation and a contemporary environmental and oceanographic complexity; hence, it is a suitable system to test the effect of historical and contemporary factors on genomic diversity in marine species. We investigated the genomic seascape of the redhead goby (Elacatinus puncticulatus; Ginsburg, 1938), a cryptobenthic marine fish, to gain insights into the historical and contemporary drivers shaping its population structure in the GC. A total of 4802 SNPs markers were analysed, with 3775 loci classified as neutral markers and 27 as outlier markers potentially under selection. Both markers demonstrated population structure, with the neutral markers showing two main groups corresponding to northern and southern locatities. The outlier markers identified an additional genetic group emerging in the central area of the sampled localities. Genetic differentiation between the North and South regions and historical demographic simulations was consistent with ancient divergence (1.04 Mya) and secondary contact (0.15 Mya). The genomic environmental association analysis revealed a possible adaptive scenario linked to ocean temperature. The study highlights the importance of historical events, contemporary environmental factors, and oceanographic circulation in shaping the genetic structure of E. puncticulatus populations in the GC., (© 2025 John Wiley & Sons Ltd.)

Background: The giant keyhole limpet Megathura crenulata is a gastropod mollusk (Fissurella superfamily) that is endemic to the eastern Pacific coast from southern California, USA, to Baja California Sur, Mexico. M. crenulata is socioeconomically important as it produces a potent immune-stimulating protein, called Keyhole Limpet Hemocyanin, which is extracted in vivo and utilized for vaccine development. However, ecological studies are scarce and genetic knowledge of the species needs to be improved. Our objectives were to assemble and annotate the mitogenome of M. crenulata , and to assess its phylogenetic relationships with other marine gastropods and to evaluate its population genetic diversity and structure., Methods: Samples were collected for mitogenome assembly ( n = 3) spanning its geographic range, Puerto Canoas (PCA) and Punta Eugenia (PEU), Mexico, and California (CAL), USA. Total DNA was extracted from gills sequenced using Illumina paired-end 150-bp-read sequencing. Reads were cleaned, trimmed, assembled de novo , and annotated. In addition, 125 samples from eight locations were analyzed for genetic diversity and structure analysis at the 16s rRNA and COX1 genes., Results: The M. crenulata mitogenomes had lengths of 16,788 bp (PCA) and 16,787 bp (PEU) and were composed of 13 protein-coding regions, 22 tRNAs, two rRNAs, and the D-Loop region. In terms of phylogeographic diversity and structure, we found a panmictic population that has experienced recent demographic expansion with low nucleotide diversity (0.002), high haplotypic diversity (0.915), and low φ ST (0.047)., Conclusions: Genetic insights into the giant keyhole limpet provides tools for its management and conservation by delimiting fishing regions with low genetic diversity and/or genetically discrete units.

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., (© The Author(s) 2023. Published by Oxford University Press on behalf of The American Genetic Association. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The totoaba (Totoaba macdonaldi) is an emblematic species endemic to the Gulf of California, which has been protected since the mid-70 s by Mexican and international laws. For the present study, 153 totoaba individuals were collected from 2011 to 2014, on which gonad histology analyses were carried out. We identified six ovarian phases and eleven oocyte subphases in the gonad development of females; in males, four development phases were identified. The totoaba is an iteroparous species based on the number of breeding opportunities. According to the organization of the ovary and the presence of oocyte subphases, ovarian dynamics can be considered asynchronous, as demonstrated by the multimodal distribution of oocyte diameter. The totoaba is a batch spawner that releases oocytes over several months. The reproductive period spans from February to May, with a reproductive peak in March. Likewise, the gonadosomatic index showed that the reproductive activity of totoaba peaked in March and April. The female:male sex ratio, although variable throughout the sampling period, yielded an overall value of 0.89:1, with non-significant differences between the number of females and males (P > 0.05). The length at first sexual maturity (L 50% ) was 1 354 mm TL for females and 1 299 mm TL for males. The average fecundity was 2 662 626 (standard error, s.e., 1 021 124) oocytes, and the average relative fecundity was 99 (s.e. 22) oocytes g -1 (ovary-free). The mean and maximum oocyte diameter showed a positive and non-significant (P > 0.05) relationship with the mean sea surface temperature., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

This study analyzed total mercury (THg), and selenium (Se) in edible tissues of white shrimp (Litopenaeus vannamei), blue shrimp (L. stylirostris) and brown shrimp (F. californiensis), from three states of the Northwest of Mexico in September and October 2017. Concentrations of THg and Se in the muscle were between 0.026 and 0.829 and 0.126-1.741 µg/g dry weight (dw), respectively. Significant differences were observed among Hg concentration of Sonora and Nayarit and among Se concentration of Sinaloa and Nayarit. In addition, the health risk assessment (HQ) in the three species of shrimp was between 0.550 and 0.607. All Se:Hg molar ratios were > 1 and positive HBV Se values that showed that shrimp from Northwest of Mexico does not represent a risk to human health., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The chilhuil sea catfish ( Bagre panamensis ) is an ecologically relevant species contributing to the structure, organization, and functioning of the ecosystems it inhabits. Also, it is an important artisanal fishery resource in the Mexican Pacific coast. This study aimed to determine the genetic diversity, population structure, and historical demography of B. panamensis in the Mexican Pacific. The mitochondrial DNA was amplified from two distinct regions, r16S and COI, resulting in an 1142 bp of the concatenated genes. Low genetic diversity levels were detected for r16S ( H  = 12; h =  0.131 ; π  =  0.0003 ) and high genetic diversity levels for COI ( H  = 57; h =  0.9128; π = 0.0039 ) and the concatenated gene fragments ( H  = 62; h =  0.9307; π = 0.0023 ). Population structure analysis indicated 'panmixia' for B. panamensis along the Mexican Pacific. Furthermore, historical demographic analysis (Tajima's D , Fu's F s, mismatch distribution, and Bayesian Skyline plot analyses) supported a population expansion scenario for the studied species.

Fatty acid desaturases are key enzymes involved in unsaturated fatty acid biosynthesis, which insert double bonds at specific positions of fatty acids, playing a pivotal role in unsaturated fatty acid synthesis required for membrane lipid fluidity. The ∆5 and ∆6 desaturases are responsible for producing long chain-polyunsaturated fatty acids (LC-PUFA) through their precursors α-linolenic acid and linoleic acid in organisms lacking or with very low ability to synthesize LC-PUFA by themselves. Extensive studies of fatty acid desaturases are available in model organisms, such as humans and mouse; however, the diversity of these genes in the marine biodiversity is less known. This study performed an exhaustive analysis to identify the ∆5 and ∆6 desaturases in the available marine genomes in databases, as well as transcriptomes and EST databases, and their coding sequences were compared to the well-characterized ∆5 and ∆6 desaturases from humans. The FADS1 and FADS2 genetic structures are well conserved among all the organisms analyzed. A common amino acid pattern was identified to discriminate between ∆5 and ∆6 desaturases. The analysis of the conserved motif involved in catalysis showed that 20% of the desaturases, ∆5 and ∆6, have lost motifs required for catalysis. Additionally, bifunctional ∆5/∆6 desaturases were able to be identified by amino acid sequence patterns found in previously described enzymes. A revision of the expression profiles and functional activity on sequences in databases and scientific literature provided information regarding the function of these marine organism enzymes., Competing Interests: Declaration of competing interest The authors declare that there is no conflict of interest., (Copyright © 2020 Elsevier Inc. All rights reserved.)

The almaco jack, Seriola rivoliana, is a circumtropical pelagic fish of importance both in commercial fisheries and in aquaculture. To understand levels of genetic diversity within and among populations in the wild, population genetic structure and the relative magnitude of migration were assessed using mtDNA sequence data and single nucleotide polymorphisms (SNPs) from individuals sampled from locations in the Pacific and Atlantic Oceans. A total of 25 variable sites of cytochrome c oxidase subunit 1 and 3678 neutral SNPs were recovered. Three genetic groups were identified, with both marker types distributed in different oceanic regions: Pacific-1 in central Pacific, Pacific-2 in eastern Pacific and Atlantic in western Atlantic. Nonetheless, the analysis of SNP identified a fourth population in the Pacific coast of Baja California Sur, Mexico (Pacific-3), whereas that of mtDNA did not. This mito-nuclear discordance is likely explained by a recently diverged Pacific-3 population. In addition, two mtDNA haplogroups were found within the western Atlantic, likely indicating that the species came into the Atlantic from the Indian Ocean with historical gene flow from the eastern Pacific. Relative gene flow among ocean basins was low with r m < 0.2, whereas in the eastern Pacific it was asymmetric and higher from south to north ( r m > 0.79). The results reflect the importance of assessing genetic structure and gene flow of natural populations for the purposes of sustainable management., (© 2020 Fisheries Society of the British Isles.)

Effective fishery management strategies should be based on stock delimitation and knowledge of the spatial scale at which species are distributed. However, a mismatch often occurs between biological and management units of fishery resources. The green abalone ( Haliotis fulgens ) supports an important artisanal fishery in the west coast of the Baja California Peninsula (BCP), Mexico, which has shown a declining tendency despite the several management measures. Thus, the aim of this study was to characterize the spatial patterns of neutral genomic variation of green abalone along the BCP to test whether the genomic structure patterns support the current green abalone management areas. To test this hypothesis, a set of 2,170 putative neutral single nucleotide polymorphisms discovered by a double digest restriction-site associated DNA approach was used on 10 locations along the BCP. The results revealed a population structure with three putative groups: Guadalupe Island and northern and southern BCP locations. The contemporary gene flow might be explained by local oceanographic features, where it is bidirectional within the southern region but with a predominant southward flow from the northern region. These findings indicated that the administrative areas did not match the biological units of H. fulgens fishery; hence, the stock assessment and management areas should be revised., Competing Interests: The authors declare that they have no competing interests., (© 2020 Mejía-Ruíz et al.)

Conservation of the evolutionary legacy of endangered species is a key component for long-term persistence. Totoaba is a long-lived fish endemic to the Gulf of California and is considered critically endangered. There is currently a debate concerning its conservation status and whether it can be used as a fishery resource. Unfortunately, basic information on biological and genetic population structure of the species is lacking. We sampled 313 individuals and employed 16 microsatellite loci and 3 mitochondrial DNA markers (16S, 547 pb; COI, 619 pb; control region, 650 pb) to assess population structure and demography of totoaba in the Gulf of California, with samples from locations that encompass nearly all of its recognized geographic distribution. We could not reject a hypothesis of panmixia for totoaba, using nuclear or mitochondrial markers. Demographic analysis of mtDNA suggests a sudden population expansion model. The results have important implications for totoaba conservation because poaching is a significant conservation challenge and could have additive negative effects over the single population of totoaba in the Gulf of California., (© The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Fisheries genomics is an emerging field that advocates the application of genomic tools to address questions in fisheries management. Genomic approaches bring a new paradigm for fisheries management by making it possible to integrate adaptive diversity to understand fundamental aspects of fisheries resources. Hence, this review is focused on the relevance of genomic approaches to solve fisheries-specific questions. Particularly the detection of adaptive diversity (outlier loci) provides unprecedented opportunity to understand bio-complexity, increased power to trace processed sample origin to allow enforcement and the potential to understand the genetic basis of micro-evolutionary effects of fisheries-induced evolution and climate change. The understanding of adaptive diversity patterns will be the cornerstone of the future links between fisheries and genomics. These studies will help stakeholders anticipate the potential effects of fishing or climate change on the resilience of fisheries stocks; consequently, in the near future, fisheries sciences might integrate evolutionary principles with fisheries management., (© The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.)