Microplastics in the Indian and South Atlantic oceans translocate to gills, digestive glands, and muscle of the chokka squid Loligo reynaudii.

Comparative microplastic (MP) data for cephalopods between oceans is scarce. Our aim was to quantify, characterise, and compare MPs in gills, digestive gland, and mantle of chokka squid from the South Atlantic Ocean (SAO) and Indian Ocean (IO) off the coast of South Africa. South African squid had more MPs compared with other studies (means = 2.0 and 0.4 in SAO and IO squid mantle, respectively). Blue fibres were dominant. Identifiable MPs were polyethylene. Despite IO water having higher MP concentrations than the SAO, SAO squid had higher MP concentrations. Dilution by growth is the likely reason for the lower MP concentrations. Fibres were shorter in SAO than IO squid. However, we could not explain why fibre and mantle lengths from both oceans were positively correlated. Squid may not be the best indicator of marine MPs. The characteristics of MPs in squid can be used to track stocks and migrations.

Lipid-correction models for δ13C values across small pelagic fishes (Clupeiformes) from the Atlantic Ocean.

The interpretation of δ13C values in trophic ecology requires standardization of the lipid content of organisms estimated through their C:N ratio. To avoid time-consuming lipid extractions, the use of mathematical corrections has been developed for many years, and the conclusions generally point in the direction of species-specific adjustment of the models. This study aimed at defining the maximum taxonomic level required to obtain the best corrected δ13C values in small pelagic fish of the order Clupeiformes. δ13C values of six species were analyzed bulk and lipid-free, and were used to fit and validate linear and mass-balance models at different taxonomic levels. Despite a species effect combined with the C:N ratio effect, the corrected δ13C values produced by a global model for the Clupeiformes were as good as or better when compared to lipid-free samples than those produced by species-specific models, paving the way for possible generalization to other species in this order. At the order level, the linear model outperformed the mass-balance model.

The sardine run in southeastern Africa is a mass migration into an ecological trap.

The KwaZulu-Natal sardine run, popularly known as the "greatest shoal on Earth," is a mass migration of South African sardines from their temperate core range into the subtropical Indian Ocean. It has been suggested that this represents the spawning migration of a distinct subtropical stock. Using genomic and transcriptomic data from sardines collected around the South African coast, we identified two stocks, one cool temperate (Atlantic) and the other warm temperate (Indian Ocean). Unexpectedly, we found that sardines participating in the sardine run are primarily of Atlantic origin and thus prefer colder water. These sardines separate from the warm-temperate stock and move into temporarily favorable Indian Ocean habitat during brief cold-water upwelling periods. Once the upwelling ends, they find themselves trapped in physiologically challenging subtropical habitat and subject to intense predation pressure. This makes the sardine run a rare example of a mass migration that has no apparent fitness benefits.

Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run.

During austral winter, the southern and eastern coastlines of South Africa witness one of the largest animal migrations on the planet, the KwaZulu-Natal sardine run. Hundreds of millions of temperate sardines, Sardinops sagax, form large shoals that migrate north-east towards the subtropical Indian Ocean. Recent studies have highlighted the role that genetic and environmental factors play in sardine run formation. In the present study, we used massively parallel sequencing to assemble and annotate the first reference transcriptome from the liver cells of South African sardines, and to investigate the functional content and transcriptomic diversity. A total of 1,310,530 transcripts with an N50 of 1578 bp were assembled de novo. Several genes and core biochemical pathways that modulate energy production, energy storage, digestion, secretory processes, immune responses, signaling, regulatory processes, and detoxification were identified. The functional content of the liver transcriptome from six individuals that participated in the 2019 sardine run demonstrated heterogeneous levels of variation. Data presented in the current study provide new insights into the complex function of the liver transcriptome in South African sardines.

Polyhalogenated Compounds (Halogenated Natural Products and POPs) in Sardine (Sardinops sagax) from the South Atlantic and Indian Oceans.

Halogenated natural products (HNPs) and persistent organic pollutants (POPs) were quantified in South African sardines (Sardinops sagax) from one site in the South Atlantic Ocean and one in the Indian Ocean. At both sites, HNPs [2,3,3',4,4',5,5'-heptachloro-1'-methyl-1,2'-bipyrrole (Q1), mixed halogenated compound 1 (MHC-1), 2,4,6-tribromoanisole (2,4,6-TBA), 2'-MeO-BDE 68 (BC-2), and 6-MeO-BDE 47 (BC-3)] were 1 order of magnitude higher concentrated than anthropogenic POPs [mainly polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethane (DDT), ∼3 ng/g lipids]. MHC-1 and Q1 were the major HNPs in the samples from both sites, contributing with up to 49 and 52 ng/g lipids, respectively. The same 1,1-dichloro-2,2-bis(4-chlorophenyl)ethane (p,p'-DDE)/PCB ratio suggested that the major POPs were evenly distributed at both sites. Different ratios of Q1/MHC-1 in the samples from the Indian (∼2:1) and South Atlantic (∼1:1) Oceans indicated that the occurrence of HNPs in seafood is difficult to predict and should be investigated more in detail. The PCB levels in sardines were found to pose no risk to human consumers, whereas HNPs could not be evaluated because of the lack of toxicological data.

Halogenated natural products and anthropogenic persistent organic pollutants in chokka squid (Loligo reynaudii) from three sites along the South Atlantic and Indian Ocean coasts of South Africa.

Chokka squid (Loligo reynaudii) from three sites along the South African coast were analyzed for halogenated natural products (HNPs) and anthropogenic persistent organic pollutants (POPs). HNPs were generally more than one order of magnitude more abundant than POPs. The most prevalent pollutant, i.e. the HNP 2,3,3',4,4',5,5'-heptachloro-1'-methyl-1,2'-bipyrrole (Q1), was detected in all chokka squid samples with mean concentrations of 105, 98 and 45 ng/g lipid mass, respectively, at the Indian Ocean (site A), between both oceans (site B) and the South Atlantic Ocean (site C). In addition, bromine containing polyhalogenated 1'-methyl-1,2'-bipyrroles (PMBPs), 2,4,6-tribromophenol (2,4,6-TBP, up to 28 ng/g lipid mass), polybrominated methoxy diphenyl ethers, MHC-1, TBMP and other HNPs were also detected. Polychlorinated biphenyls (PCBs) were the predominant class of anthropogenic POPs. PCB 153 was the most abundant PCB congener in chokka squid from the Indian Ocean, and PCB 138 in samples from the South Atlantic Ocean and between both oceans.

Parasite community structure as a predictor of host population structure: An example using Callorhinchus capensis.

This paper describes the parasite community structure of the Cape elephant fish or St Joseph shark (Callorhinchus capensis) caught off the West and South Coast of South Africa between 2010 and 2015. These data were used to build species accumulation curves (SAC) and calculate biodiversity indices including rarefied species richness, Shannon Weiner's diversity index, Simpson's index and Pielou's J index. The biodiversity indices were correlated with the host's biological data to determine how these affected the parasite community structure and provide insight into the host's population structure. The parasites identified in C. capensis (n = 259) include a cestode (Gyrocotyle plana), two monogeneans (Callorhynchicotyle callorhynchi and Callorhinchicola multitesticulatus), an isopod (Anilocra capensis) and a leech (Branchellion sp.). Gyrocotyle plana was the most prevalent at 71.43% and the monogenean C. callorhynchi had the highest mean abundance (1.55 ±â€¯0.45 parasites.fish-1) and the highest mean infection intensity (4.79 ±â€¯0.66 parasites.infected fish-1). The SAC and biodiversity measures indicate a uniform parasite community across the sampled host population, suggesting a highly interactive shark community with no evidence for population structure. These results show that parasite community structure can be used to infer their host's population structure.

Observations on the biology and seasonal variation in feeding of the east coast round herring Etrumeus wongratanai (Clupeiformes), off Scottburgh, KwaZulu-Natal, South Africa.

The basic biology and ecology of the South African east coast round herring Etrumeus wongratanai was investigated from samples of fish collected between 2013 and 2016. This species is short-lived and reaches a maximum of 3 years of age, with rapid growth in its first year of life. It reproduces from June to December (austral summer) and condition factor was lowest in May through to August and increased from September, probably reflecting the physiological strain before and during spawning. Fish larvae were the most important food items consumed during summer, whereas eucalanid copepods were the most important prey at other times of the year. Stable-isotope data suggest that there are gradual changes in the trophic level with increasing fish size, δ15 N and δ13 C values also differed between seasons. The results obtained here are compared with those of other Etrumeus species, regionally and globally.

Mitochondrial DNA is unsuitable to test for isolation by distance.

Tests for isolation by distance (IBD) are the most commonly used method of assessing spatial genetic structure. Many studies have exclusively used mitochondrial DNA (mtDNA) sequences to test for IBD, but this marker is often in conflict with multilocus markers. Here, we report a review of the literature on IBD, with the aims of determining (a) whether significant IBD is primarily a result of lumping spatially discrete populations, and (b) whether microsatellite datasets are more likely to detect IBD when mtDNA does not. We also provide empirical data from four species in which mtDNA failed to detect IBD by comparing these with microsatellite and SNP data. Our results confirm that IBD is mostly found when distinct regional populations are pooled, and this trend disappears when each is analysed separately. Discrepancies between markers were found in almost half of the studies reviewed, and microsatellites were more likely to detect IBD when mtDNA did not. Our empirical data rejected the lack of IBD in the four species studied, and support for IBD was particularly strong for the SNP data. We conclude that mtDNA sequence data are often not suitable to test for IBD, and can be misleading about species' true dispersal potential. The observed failure of mtDNA to reliably detect IBD, in addition to being a single-locus marker, is likely a result of a selection-driven reduction in genetic diversity obscuring spatial genetic differentiation.

Bottom-up effects of a no-take zone on endangered penguin demographics.

Marine no-take zones can have positive impacts for target species and are increasingly important management tools. However, whether they indirectly benefit higher order predators remains unclear. The endangered African penguin (Spheniscus demersus) depends on commercially exploited forage fish. We examined how chick survival responded to an experimental 3-year fishery closure around Robben Island, South Africa, controlling for variation in prey biomass and fishery catches. Chick survival increased by 18% when the closure was initiated, which alone led to a predicted 27% higher population compared with continued fishing. However, the modelled population continued to decline, probably because of high adult mortality linked to poor prey availability over larger spatial scales. Our results illustrate that small no-take zones can have bottom-up benefits for highly mobile marine predators, but are only one component of holistic, ecosystem-based management regimes.

Accommodating dynamic oceanographic processes and pelagic biodiversity in marine conservation planning.

Pelagic ecosystems support a significant and vital component of the ocean's productivity and biodiversity. They are also heavily exploited and, as a result, are the focus of numerous spatial planning initiatives. Over the past decade, there has been increasing enthusiasm for protected areas as a tool for pelagic conservation, however, few have been implemented. Here we demonstrate an approach to plan protected areas that address the physical and biological dynamics typical of the pelagic realm. Specifically, we provide an example of an approach to planning protected areas that integrates pelagic and benthic conservation in the southern Benguela and Agulhas Bank ecosystems off South Africa. Our aim was to represent species of importance to fisheries and species of conservation concern within protected areas. In addition to representation, we ensured that protected areas were designed to consider pelagic dynamics, characterized from time-series data on key oceanographic processes, together with data on the abundance of small pelagic fishes. We found that, to have the highest likelihood of reaching conservation targets, protected area selection should be based on time-specific data rather than data averaged across time. More generally, we argue that innovative methods are needed to conserve ephemeral and dynamic pelagic biodiversity.

Effect of maternal fat reserves on the fatty acid composition of sardine (Sardina pilchardus) oocytes.

We compared the fatty acid (FA) composition of the muscle and gonads of female Iberian sardines with hydrated oocytes collected during the 2002/03 spawning season off southern Portugal (November and February) and off western Portugal (February). Sardine condition and total FA concentration in the muscle decreased between the two sampling dates, while the gonadosomatic index was similar between samples. Total monounsaturated FA concentrations in sardine gonads were different for the three samples while saturated and polyunsaturated FA concentrations were similar. Significant linear relations were found between FA concentrations in female muscle and oocytes, including eicosapentaenoic acid (EPA; 20:5n-3) and arachidonic acid (AA; 20:4n-6), both being essential for normal larval development. The concentration of docosahexaenoic acid (DHA; 22:6n-3) in oocytes was independent on muscle concentration, probably resulting from its selective transfer to the oocytes. The EPA/DHA ratio was highly conserved in sardine tissues, while DHA/AA and EPA/AA ratios varied significantly between samples. These results indicate that the FA content of eggs produced by sardines varies throughout the spawning season, egg FA concentrations decreasing as females lose condition, and FA composition also shows spatial variability. Both types of variability may have a significant impact on egg quality, particularly on the amount of reserves available to larvae affecting their resistance to starvation, and the appropriate FA composition required for normal growth.