Microchemical analyses of fish otoliths have revolutionized fisheries science. Molecules deposited within otoliths may originate from ambient water and diet, with molecular concentrations being subject to subsequent physiological alteration after exposure. Analyses of otolith microstructure and incorporation of inorganic elements have led to major advances in stock assessment and fisheries ecology. However, the use of otoliths for microchemical analyses has drawbacks. Specifically, otolith removal from live specimens requires specimen sacrifice, which may be forbidden in the case of protected species. In addition, otoliths rarely contain sufficient concentrations of organic matter to allow reconstruction of food-web relationships via multiple stable isotopes, and otolith microstructure can be difficult to interpret in some species. Here, we review alternatives to otoliths that can provide microchemical analytes for life-history studies in fishes. Our focus is to describe advantages and disadvantages to the use of each alternative structure, with particular attention paid to trace-element analysis for inorganic matrices and stable-isotope analysis for organic ones. In general, the chronological analysis of elemental and isotopic values within each structure depends on the inert nature (or lack of molecular turnover) of the tissue. Structures with high turnover rates or those that are metabolically active will not effectively record elemental or isotopic compositions over time. Here, we provide an assessment of the use of bony endoskeleton, fin spines, fin rays, scales, and eye lenses as alternatives or complements to fish otolith analysis.

Species invasions in marine ecosystems pose a threat to native fish communities and can disrupt the food webs that support valuable commercial and recreational fisheries. In the Gulf of Mexico, densities of invasive Indo‐Pacific Lionfish, Pterois volitans and P. miles, are among the highest in their invaded range. In a workshop setting held over a 2‐week period, we adapted an existing trophic dynamic model of the West Florida Shelf, located in the eastern Gulf of Mexico, to simulate the lionfish (both species) invasion and community effects over a range of harvest scenarios for both lionfish and native predators. Our results suggest small increases in lionfish harvest can reduce peak biomass by up to 25% and also that reduced harvest of native reef fish predators can lead to lower lionfish densities. This model can help managers identify target harvest and benefits of a lionfish fishery and inform the assessment and management of valuable reef fish fisheries.

Artificial reefs are used to enhance populations of marine organisms, but relatively few studies have quantitatively evaluated which attributes of reef structure are most critical in determining whether assemblages of organisms on artificial reefs are similar to those on natural reefs. Using five pairs of artificial and natural reefs that spanned 225 km in the Southern California Bight, we evaluated how well fish assemblages on artificial reefs mimicked those on natural reefs and which attributes of reefs best predicted assemblage structure. Along underwater visual transects, we quantified fish species richness, density, and size structure, as well as substrate structure (rugosity and cover of substrate types), giant kelp density, and invertebrate density. Artificial reefs that were more similar in physical structure to natural reefs (low relief, low rugosity, and composed of small- to medium -sized boulders) supported fish assemblages that were similar to those on natural reefs. Fish species richness was not significantly different between artificial and natural reefs, but density and biomass tended to be higher on average on artificial reefs, body size was slightly smaller, and assemblage structure differed between the two reef types. Generally, artificial reefs extended higher off the seabed, were made of larger boulders, had higher rugosity, harboured more invertebrates, and supported less giant kelp. At both the within-reef (transect) and whole-reef scales, fish density and biomass were positively correlated with complex substrate structure, positively correlated with invertebrate density, and negatively correlated with giant kelp abundance, which was sparse or absent on most artificial reefs. Our results indicate that artificial reefs can support fish assemblages that are similar to those found on natural reefs if they are constructed to match the physical characteristics of natural reefs, or they can be made to exceed natural reefs in some regards at the expense of other biological attributes.

The extent to which artificial reefs may be useful for mitigation of environmental impacts, fisheries management, and conservation depends in part upon how well the organisms that live on them fare. We tested whether fish living on artificial reefs were in similar condition (weight-at-length), grew, foraged, reproduced, and produced tissue at rates similar to those on natural reefs. We studied five artificial–natural reef pairs spread over >200 km in the Southern California Bight. Underwater visual transects were used to quantify density and size structure of four target species (Paralabrax clathratus, Paralabrax nebulifer, Semicossyphus pulcher, and Embiotoca jacksoni), which were also collected to measure foraging success, condition, growth, reproductive output, and tissue production. Generally, fish living on artificial reefs fared as well or better than those on natural reefs, with some exceptions. Semicossyphus pulcher fared better on artificial reefs, having higher foraging success, fecundity, densities, and tissue production. Embiotoca jacksoni grew faster on natural reefs, and P. nebulifer was in slightly better condition on natural reefs. Total fish tissue production tended to be higher on artificial reefs than on natural reefs, though this pattern was not evident on all reef pairs. Tissue production was positively correlated with the abundance of large boulders, which was higher on artificial reefs than natural reefs. The similar or greater production of fish tissue per cubic metre on artificial reefs relative to natural reefs indicates that these artificial habitats are valuable in producing fish biomass. Fish living on artificial reefs fared as well as those living on natural reefs, indicating that well-designed artificial reefs can be useful tools for mitigation, conservation, and fisheries management.