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.
•Small pelagic fish populations respond strongly to bottom-up forcing.•A review of greater than 900 studies from 2001 to 06 and 2011–16 identified recent research trends.•Knowledge gaps include ...bottom-up effects on reproduction, physiology, and disease.•Robust projections of how climate change will affect bottom-up processes are needed.•We recommend research future avenues and renewed international collaboration.
Small pelagic fish (SPF) play extremely important ecological roles in marine ecosystems, form some of the most economically valuable fisheries resources, and play a vital role in global food security. Due to their short generation times and tight coupling to lower trophic levels, populations of SPF display large boom-and-bust dynamics that are closely linked to climate variability. To reveal emerging global research trends on SPF as opposed to more recently published, ecosystem-specific reviews of SPF, we reviewed the literature published in two, 6-year periods in the new millennium (2001–2006, and 2011–2016) straddling the publication of a large, global review of the dynamics of SPF in 2009. We explored intrinsic and extrinsic (bottom-up) factors influencing the dynamics of SPF such as anchovies, sardines, herrings and sprats within the sub-order Clupeidae. Published research efforts within 16 different biogeographic ocean regions were compiled (more than 900 studies) and compared to identify i) new milestones and advances in our understanding, ii) emerging research trends and iii) remaining gaps in knowledge. Studies were separated into 5 categories (field, laboratory, mesocosms, long-term statistical analyses and spatially-explicit modelling) and discussed in relation to 10 bottom-up categories including 5 abiotic factors (temperature, salinity, pH, dissolved oxygen, density), 3 physical processes (advection, turbulence, turbidity) and 2 biotic factors (prey quantity and quality). The peer-reviewed literature reflects changes in the number of studies between the two time periods including increases (Mediterranean Sea, Humboldt Current) and decreases (Australia, Benguela Current). Our review highlights i) gaps in ecological knowledge on young juveniles and, in general, on the impacts of hypoxia and heatwaves on SPF, ii) the utility of paleo studies in exploring population drivers, iii) the continued need to develop spatially-explicit, full life-cycle models, iv) the importance of exploring how density-dependent processes impact vital rates (growth, survival, reproduction), and v) the benefits of international collaboration for knowledge transfer and building unifying hypotheses on the role of bottom-up factors and processes that regulate SPF populations.
1. Remote-sensing measurements of marine primary productivity are widely used to predict the distribution and movements of marine top predators, despite the fact that predators do not feed directly ...on phytoplankton but several trophic levels higher up the food chain. 2. To test for potential links between primary productivity and top-predator feeding hotspots, we assessed spatial match-mismatch across four trophic levels of the Benguela upwelling zone (south-east Atlantic). The food chain studied consisted of phytoplankton, zooplankton (copepods), pelagic fish (anchovies and sardines) and two top predators (Cape gannets Morus capensis and human fisheries). 3. Remote-sensing data of sea-surface temperature (SST) and chlorophyll_a concentration were used as indices of phytoplankton abundance throughout the study area. Copepod biomass and pelagic fish density were determined during at-sea surveys in the South African section of the Benguela using net tows and hydro-acoustics, respectively. Seabird (Cape gannet) home ranges and foraging zones were assessed from two Namibian breeding colonies (Mercury and Ichaboe) and two South African colonies (Lambert's Bay and Malgas) using global positioning system (GPS) tracking. Industrial fishing for anchovies and sardines was investigated using South African landing statistics and logbooks. 4. Our spatial analyses revealed a strong match of seabird at-sea habitat and zones of high primary productivity throughout the southern Benguela. Conversely, there was a marked spatial mismatch between copepods and pelagic fish, as well as between pelagic fish, seabirds and human fisheries: copepods were present in the southern Benguela but pelagic fish usually feeding upon them were located further east (Indian Ocean), outside of the Benguela sensu stricto. Consequently, the majority of these pelagic fish were out of reach for seabirds and fisheries confined to the southern Benguela. 5. Synthesis and applications. Our study demonstrates the impact of an ecosystem shift across one of the world's most productive marine ecosystems and highlights the limitations of using remote-sensed patterns of primary productivity to interpret the foraging behaviour of marine top predators. These findings underline the importance of a better knowledge of food web spatial dynamics to support ecosystem-based fisheries management and the conservation of marine top predators.
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.
•Microplastics for tracking fish stocks.•Microplastic move through ocean via bio-assisted transfer.•Comparison of microplastics in organisms between two oceans.•Dilution by growth of microplastics in Loligo reynaudii.
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.
•Changes in δ13C values following lipid removal depend on bulk C:N ratio and species.•Corrected δ13C values from linear and mass balance models were similar.•Linear lipid correction model can be applied at the Clupeiforme order level.•Clupeiforme order has an average lipid-free C:N ratio of 3.1
This paper examines whether the ranges of occurrence of anchovy and sardine eggs have changed off the South African coast in recent years, and whether this could be linked to changes in sea surface ...temperature (SST). We used a single parameter quotient analysis with randomization to estimate the preferred and tolerated SST ranges of the spawning habitats of anchovy and sardine in the southern Benguela over the period 1988–2009. Previous studies have reported long‐term change in SST off the South African coast, and our analysis was aimed at determining whether spawning habitat selection by these small pelagic fish tracked such change. The analysis used data on egg occurrence collected concurrently with in situ SST data during annual surveys of pelagic fish biomass conducted along the South African coast. Results show that anchovy typically, but not always, spawn in warmer waters (17.0–23.0°C) than sardine do (16.0–22.0°C), and sardine almost always showed a wider SST tolerance range than did anchovy, over the time‐series. The analysis further suggests evidence of an increase in the surface temperature conditions along the South African coast recently; the spawning patterns of anchovy (Engraulis encrasicolus) and sardine (Sardinops sagax) appear to track these changes through time. Therefore, the spawning habitat preferences of anchovy and sardine in the southern Benguela have changed in recent years, but this is unlikely to be due to warming alone.
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.
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•HNPs were more abundant than POPs in squid from three marine sites in South Africa.•Heptachloro-1′-methyl-1,2′-bipyrrole (Q1) was predominant in all samples.•HNPs except TBP were more abundant in squid from the Indian than the Atlantic Ocean.•PCBs were the most relevant anthrophonic contaminants in all samples.•PCB 153/138 ratio in squid was >1 in the Indian Ocean and <1 in the Atlantic Ocean.
This study applied a previously used Lagrangian individual‐based model (IBM) for sardine in the Southern Benguela to an improved and more robust hydrodynamic model to investigate whether a more ...representative spatial coverage, greater horizontal and vertical resolution, more realistic winds and improved representation of mesoscale features such as eddies and filaments would give different results for transport and retention of early life stages. Despite major differences between the old and new hydrodynamic models, overall the IBM results were quite similar to the previous southern Benguela sardine IBM study. This surprising result indicates that it is the macroscale circulation features resolved by the two hydrodynamic models that are controlling transport and retention of sardine early life stages. The contribution of transient mesoscale features such as eddies and filaments appears to be less important when transport patterns are averaged over the 21‐year‐long experiment. Another aim of this study was to better estimate the contribution of south coast spawning to west coast sardine recruitment. This was possible because of an eastward extension of the geographical domain of the new hydrodynamic model which provided a more realistic representation of the south coast spawning ground. Three main spawning and nursery area systems, similar to those identified in the previous sardine IBM, were identified: west coast and west coast (WC‐WC), south coast and west coast (SC‐WC), and south coast and south coast (SC‐SC). Spawning area proved to be an important determinant of modelled retention and transport success, with spawning depth also playing an important role on the west coast. The main difference observed from the previous study was an increase in the average percentage of particles released on the south coast and transported to the west coast (P0, 17.4%). This indicates more connectivity between the southern and western sardine stocks than previously thought and is therefore important for fishery management. Standardized anomalies from the modelled retention/transport were compared with recruitment estimates from stock assessment models but there was no correlation between the two sets of anomalies. However, a significant correlation was observed between the modelled retention/transport anomalies for the west coast and total cumulative upwelling anomalies for the Southern Benguela (r = −0.67, p < .001).
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, δ15N and δ13C values also differed between seasons. The results obtained here are compared with those of other Etrumeus species, regionally and globally.
1. Climate change and fishing impact marine ecosystems, potentially modifying the availability of small pelagic fish to marine top predators. Some seabirds that primarily rely upon these resources ...have switched to feeding on fishery waste. It has therefore been argued that seabirds might become dependent upon this artificial resource. 2. To test this hypothesis, we studied the foraging behaviour of Cape gannets Morus capensis breeding off the coast of South Africa using high-resolution Global Positioning System-tracking in relation to the availability of pelagic fish assessed by acoustic at-sea surveys, and fishing effort by the two main south African fisheries (purse seiners that compete with seabirds for pelagic fish, and demersal trawlers that process fish at sea and discharge fish waste) tracked with vessel monitoring systems. Conjoint seabird, fish and fisheries information were analysed at mesoscale (c. 100 km) and sub-mesoscale (c. 10 km) in years of high (2002), medium (2009) and low (2005) pelagic fish biomass within gannets' foraging range. 3. We found substantial inter-annual variability in spatial use by breeding gannets, which was driven primarily by pelagic fish availability. At the mesoscale, birds and purse seiners exploited similar marine areas, but no fine-scale dependence of birds on purse seiners was detected. Crucially, fine-scale dependence of gannets upon trawlers producing fishery waste was only detected in 2005, when pelagic fish biomass was lowest, indicating a direct effect of trawlers on gannet foraging behaviour in the absence of natural prey. 4. Further overlap analyses of gannet and trawler foraging areas during 2002–2010 confirmed that breeding birds only seek trawlers when pelagic fish availability is low, strongly suggesting reversible seabird dependency upon fishery waste. 5. Synthesis and applications. Our study demonstrates that seabirds such as Cape gannets depend on fishery waste when their natural prey is scarce, but revert to feeding on natural resources whenever available, showing highly flexible foraging behaviour. These results have important implications in the context of the anticipated legislation banning at-sea disposal of fishery waste in different regions, including European seas, highlighting the necessity to concomitantly promote sustainable fishing allowing the restoration of pelagic fish stocks.
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