Fishing for Florida Bass in West Virginia: Genomic Evaluation of Florida Bass Presence and Establishing Baselines of Genetic Structure and Diversity for Native Largemouth Bass

Florida bass (Micropterus salmoides) and largemouth bass (Micropterus nigricans) are iconic sport fish that hybridize readily, influencing fishery management practices. While the Florida bass has been introduced to various U.S. states to create trophy fisheries, its genetic introgression into native populations can lead to ecological and genetic consequences. Recognizing the need to assess Florida bass presence to guide future management directions, diagnostic SNPs were genotyped for 856 putative largemouth bass across 31 sampling locations across the state of West Virginia. Florida bass controls and a reduced representative sample of 226 individuals from 19 sampling locations were sequenced using the genotype-by-sequencing dd-RAD protocol. The results from the two genomic investigations found no Florida bass ancestry in West Virginia populations, suggesting either no introduction or failed reproductive success of Florida bass in the state. Among West Virginia largemouth bass populations, unique genetic ancestries were found predominantly in introduced non-native largemouth bass populations, indicating that the only sub-structuring in the state is a result of stocking non-native ancestries into the state. Genomic diversity was found to be higher in Ohio River pools compared to inland reservoirs, as well as showing higher levels of potential inbreeding. These results underscore the need to preserve the genetic integrity of native Ohio River strain largemouth bass and prevent the introduction of the Florida bass or F1 hybrids into the Ohio River and other watersheds of West Virginia. Management recommendations include prioritizing the stocking of native strain bass to mitigate inbreeding and avoid introducing Florida bass to conserve genetic diversity.

Otolith and Genomic Data Reveal Temporal Insights Into Stocking Across a Large River Basin in a Mobile, Long-Lived Australian Freshwater Fish Species

Freshwater ecosystems and their biota are under increasing pressure from anthropogenic stressors. In response to declining fish stocks, hatchery and stocking programmes are widely implemented as core components of restoration and management strategies, with positive outcomes for some wild populations. Despite this, stocking remains contentious due to potential genetic and ecological risks to wild populations. Monitoring and evaluation of stocking outcomes are critical to ensuring the long-term sustainability of wild populations, but identification of stocked individuals post-release remains a key challenge, particularly for mobile species. In this study, we combined otolith (natal origin and age) and genomic data to identify stocked individuals and evaluate the genetic implications of stocking for a culturally and socioeconomically important and mobile freshwater fish, golden perch Macquaria ambigua (family: Percichthyidae), across Australia's Murray-Darling Basin (MDB). We also generated a chromosome-level genome assembly. Many close kin were detected across the MDB, increasing in prevalence over recent decades and mostly of hatchery origin. Rivers with many close kin were associated with low effective population sizes (Ne < 100). Genetic signatures of stocking varied according to local context, being most pronounced in but not restricted to rivers considered functionally isolated for management purposes. Where fish are stocked into rivers that are part of the connected metapopulation, there is scope to modify current stocking practices to avoid over-representation of related stocked individuals. Increased focus on the genetic diversity of stocked fish is likely to promote the long-term persistence of golden perch in the wild.

Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations

A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.

Summer Is Coming! Tackling Ocean Warming in Atlantic Salmon Cage Farming

Atlantic salmon (Salmo salar) cage farming has traditionally been located at higher latitudes where cold seawater temperatures favor this practice. However, these regions can be impacted by ocean warming and heat waves that push seawater temperature beyond the thermo-tolerance limits of this species. As more mass mortality events are reported every year due to abnormal sea temperatures, the Atlantic salmon cage aquaculture industry acknowledges the need to adapt to a changing ocean. This paper reviews adult Atlantic salmon thermal tolerance limits, as well as the deleterious eco-physiological consequences of heat stress, with emphasis on how it negatively affects sea cage aquaculture production cycles. Biotechnological solutions targeting the phenotypic plasticity of Atlantic salmon and its genetic diversity, particularly that of its southernmost populations at the limit of its natural zoogeographic distribution, are discussed. Some of these solutions include selective breeding programs, which may play a key role in this quest for a more thermo-tolerant strain of Atlantic salmon that may help the cage aquaculture industry to adapt to climate uncertainties more rapidly, without compromising profitability. Omics technologies and precision breeding, along with cryopreservation breakthroughs, are also part of the available toolbox that includes other solutions that can allow cage farmers to continue to produce Atlantic salmon in the warmer waters of the oceans of tomorrow.