The Taiwan Bank (TB) is located in the southern Taiwan Strait, where the marine environments are affected by South China Sea Warm Current and Kuroshio Branch Current in summer. The bottom water flows upward along the edge of the continental shelf, forming an upwelling region that is an essential high-productivity fishing ground. Using trophic dynamic theory, fishery resources can be converted into primary production required (PPR) by primary production, which indicates the environmental tolerance of marine ecosystems. This study calculated the PPR of benthic and pelagic species, sea surface temperature (SST), upwelling size, and net primary production (NPP) to analyze fishery resource structure and the spatial distribution of PPR in upwelling, non-upwelling, and thermal front (frontal) areas of the TB in summer. Pelagic species, predominated by those in the Scombridae, Carangidae families and Trachurus japonicus, accounted for 77% of PPR (67% of the total catch). The benthic species were dominated by Mene maculata and members of the Loliginidae family. The upwelling intensity was the strongest in June and weakest in August. Generalized additive models revealed that the benthic species PPR in frontal habitats had the highest deviance explained (28.5%). Moreover, frontal habitats were influenced by NPP, which was also the main factor affecting the PPR of benthic species in all three habitats. Pelagic species were affected by high NPP, as well as low SST and negative values of the multivariate El Niño–Southern Oscillation (ENSO) index in upwelling habitats (16.9%) and non-upwelling habitats (11.5%). The composition of pelagic species varied by habitat; this variation can be ascribed to impacts from the ENSO. No significant differences were noted in benthic species composition. Overall, pelagic species resources are susceptible to climate change, whereas benthic species are mostly insensitive to climatic factors and are more affected by NPP.

Seafood, especially the traditional one in Taiwan, is rarely sourced from a fixed species and routinely from similar species depending on their availability. Hence, the species composition of seafood can be complicated. While a DNA-based approach has been routinely utilized for species identification, a large scale of seafood identification in fish markets and restaurants could be challenging (e.g., elevated cost and time-consuming only for a limited number of species identification). In the present study, we aimed to identify the majority of fish species potentially consumed in fish markets and nearby seafood restaurants using environmental DNA (eDNA) metabarcoding. Four eDNA samplings from a local fish market and nearby seafood restaurants were conducted using Sterivex cartridges. Nineteen universal primers previously validated for fish species identification were utilized to amplify the fragments of mitochondrial DNA (12S, COI, ND5) of species in eDNA samples and sequenced with NovaSeq 6000 sequencing. A total of 153 fish species have been identified based on 417 fish related operational taxonomic units (OTUs) generated from 50,534,995 reads. Principal Coordinate Analysis (PCoA) further showed the differences in fish species between the sampling times and sampling sites. Of these fish species, 22 chondrichthyan fish, 14 Anguilliformes species, and 15 Serranidae species were respectively associated with smoked sharks, braised moray eels, and grouper fish soups. To our best knowledge, this work represents the first study to demonstrate the feasibility of a large scale of seafood identification using eDNA metabarcoding approach. Our findings also imply the species diversity in traditional seafood might be seriously underestimated and crucial for the conservation and management of marine resources.

Information regarding the oceanic environment is crucial for determining species distributions and their habitat preferences. However, in studies on crustaceans, especially swimming crabs, such information remains poorly utilized, and its effects on crab communities in the Taiwan Strait (TS) has not been well documented. The purpose of this study was to understand the relationship between the catch rates of three swimming crab species and environmental factors in the TS. We fitted generalized additive models (GAMs) to logbooks and voyage data recorder data from Taiwanese crab vessels (2011–2015), developed a species distribution model, and predicted catch rates for these three swimming crab species based on the GAM output. The chlorophyll-a (Chl-a) concentration was related to the high catch rates of Chrybdis feriatus and Portunus sanguinolentus, whereas bottom temperature (BT) was related to high catch rates of Portunus pelagicus. The variance percentages for each crab species indicated that high catch rates of C. feriatus and P. sanguinolentus occurred in a Chl-a concentration > 0.5 mg/m³, whereas P. pelagicus catch rates exhibited negative correlations with BTs > 25 °C. The model predicted high catch rates of C. feriatus in the north of the TS during autumn and winter, whereas P. pelagicus was observed to the south during summer and autumn. P. sanguinolentus was predicted to be widely distributed around the TS and distributed further to the northern area during autumn and winter. These findings revealed that each species responds to spatiotemporal environmental variations. Understanding the distributions and habitats of these three crabs is vital in fisheries resource management and conservation planning.

Mixed fisheries refer to fishing activities that catch more than one species simultaneously, and a species may be fished using different gear. A trawl fishery shares these features to exploit multiple species simultaneously, with diverse fishing gear and strategies. The situation becomes more complex when interactions among fleet dynamics, fishing activities, and fishery resources are involved and influence each other. Information regarding the operational patterns may be hidden in a set of long-term big data. This study aims to investigate the fishery structure and fleet dynamics of trawl fisheries in Taiwan for spatial planning and management, based on a long-term dataset from a management system that collects information by using voyage data recorders (VDR) and dockside observers. We applied a two-step data mining process with a clustering algorithm to classify the main groups of fishery resources and then identified 18 catch métiers based on catch composition. The target species, operation pattern, and fishing season were determined for each métier, and associated with the relevant fishery resources and the fishing gear used. Additionally, fishing effects on target species were estimated using information on fishing grounds and trajectories from VDR. The métier-based approach was successfully applied to define the six major fishery resources targeted by trawlers. We examined the key features of fishing activity associated with catch composition and spatial-temporal fishing metrics, which could be used to provide suggestions for the spatial planning and management of the mixed trawl fishery in the offshore waters of Taiwan.

Taiwan Bank (TB) is located in the southern Taiwan Strait (TS). The uplifted continental slope and bottom currents in this area result in the formation of upwelling areas, which serve as crucial fishing grounds. Climate-induced fluctuations in fish populations occur in the TS. However, how predation and competition affect the interspecies relationships in the TB ecosystem warrants clarification. In this study, we collected high-grid-resolution data on fishery activity (2013–2019) and constructed ecosystem models using Ecopath with Ecosim (EwE). Three mass-balanced models for determining the influence of El Niño–Southern Oscillation (ENSO) events on the TB ecosystem were constructed using EwE. A range of groups, including representative pelagic, benthic, and reef species, were collected for analyzing the relationship between migratory and sedentary species in terms of ecosystem structure variation due to climate change. The results demonstrated that the total system throughput (TST) was 10,556–11,122 t km⁻² year⁻¹, with an average transfer efficiency of 12.26%. According to the keystoneness index, calculated through mixed trophic impact analysis, Polydactylus sextarius and Scomber japonicus were the key species with top–down control and relatively high impact on the ecosystem in normal years. The keystone species also shifted to the predator fish Thunnus albacares and Katsuwonus pelamis during El Niño and La Niña events, respectively. Moreover, total biomass, TST, consumption, and respiration were noted to increase during ENSO events. However, during La Niña events, the diversity and connectance indexes were relatively low but pelagic species’ biomass was relatively high, whereas the biomass of most benthic and reef species was relatively high during El Niño events.

Stock enhancement, used for replenishing depleted wild finfish populations, is an aggressive approach. Stock enhancement projects in Taiwan involve black sea bream (Acanthopagrus schlegelii), a major commercial species. During 2004–2015, even management agencies conducted stock enhancement projects, leading to numerous private releases that have not been recorded. Stock enhancement by a private hatchery without accurate genetic records may lead to a genetic structure change in wild populations. Using allele frequencies at nine microsatellite loci, we studied the genetic effects of stock enhancement in 19 samples collected from populations in the hatcheries and the wild. In 458 individuals from nine hatchery samples, most populations showed weak but significant genetic differences and complex clusters in structure analysis, indicating dramatic stock change within and among hatcheries. The 10 wild populations (n = 773) also had a complex genetic composition and were genetically different among sampling sites and times. However, a simple and clear cluster in structure analysis was found for only one sampling site, which had no release history. Thus, stock enhancement with complex genetic sources helps maintain genetic diversity but dramatically changes the genetic structure within and among wild populations, especially when stock enhancement is successful.