Metabarcoding is an emerging method in which DNA barcoding is combined with next-generation sequencing to determine the biodiversity of taxonomically complex samples. We assessed the current state of DNA barcode reference databases for marine zooplankton in South Africa and undertook a metabarcoding analysis to determine the species composition of samples collected with plankton tow nets. Analysis of DNA sequences mined from the literature and in online barcode reference databases revealed incomplete records for all taxa examined. Barcode records were dominated by meroplanktonic species with commercially important life-history phases (fishes and decapod crustaceans) and by species occurring in easily accessible nearshore habitats. Holoplanktonic species were underrepresented, despite making up the bulk of zooplankton biodiversity, including most potential indicator species. Metabarcoding analysis of plankton samples could identify 45% of amplicon sequence variants to species level based on BOLD databases (123 species) and similar numbers using GenBank and the MIDORI COI classifier. Morphological analysis of samples could not achieve comparable resolution at species level, but with some exceptions it recovered similar classes of organisms to those found by metabarcoding. The need for integrative molecular/morphological studies to increase and validate barcode reference databases of key zooplankton taxa is recognised. Metabarcoding of marine zooplankton in South Africa has now been successfully undertaken and the methodology is expected to facilitate high-resolution monitoring of zooplankton biodiversity in pelagic ecosystems and accelerate the discovery of new species.

Aim - We incorporated genetic structure and life history phase in species distributionmodels (SDMs) constructed for a widespread spiny lobster, to reveal local adapta-tions specific to individual subspecies and predict future range shifts under the RCP8.5 climate change scenario. Location - Indo-West Pacific. Methods - MaxEnt was used to construct present-day SDMs for the spiny lobster Panulirus homarus and individually for the three genetically distinct subspecies of which it comprises. SDMs incorporated both sea surface and benthic (seafloor) climate layers to recreate discrete influences of these habitats during the drifting lar-val and benthic juvenile and adult life history phases. Principle component analysis (PCA) was used to infer environmental variables to which individual subspecies wereadapted. SDM projections of present-day habitat suitability were compared with pre-dictions for the year 2,100, under the RCP 8.5 climate change scenario. Results - In the PCA, salinity best explained P. h. megasculptus habitat suitability, compared with current velocity in P. h. rubellus and sea surface temperature inP. h. homarus. Drifting and benthic life history phases were adapted to different com-binations of sea surface and benthic environmental variables considered. Highly suitable habitats for benthic phases were spatially enveloped within more extensive sea surface habitats suitable for drifting larvae. SDMs predicted that present-day highlysuitable habitats for P. homarus will decrease by the year 2,100. Main conclusions - Incorporating genetic structure in SDMs showed that individualspiny lobster subspecies had unique adaptations, which could not be resolved inspecies-level models. The use of sea surface and benthic climate layers revealed therelative importance of environmental variables during drifting and benthic life history phases. SDMs that included genetic structure and life history were more informative in predictive models of climate change effects.

Bottom-trawl data collected by the RV Dr Fridtjof Nansen off Mozambique (in 1990, 2007 and 2018) and offeastern South Africa (in 2018) were analysed to investigate the distribution, abundance and size composition ofthe smooth fan lobster Ibacus novemdentatus as a potential fisheries resource. The lobsters occurred shallower(depth 53–297 m) than traditional deep-water trawl grounds, were concentrated in ‘hotspots’ at the seaward edgesof sand/mud banks at the Thukela Bank, Delagoa Bight and Sofala Bank, and exhibited segregated juvenile andadult populations. Three other high-value lobster species and several marketable teleost species occurred intrawl nets where I. novemdentatus was present. Further exploration by trawling should be considered to betterdefine hotspots of adults of this species and to investigate the contribution that I. novemdentatus could make tomixed-species commercial catches.

We report, for the first time in the wild, giant freshwater prawn Macrobrachium rosenbergii populations in East Africa. Specimens caught by fishermen in the lower reaches of the Ruvu River and Rufiji Delta in coastal Tanzania were identified based on their morphology, with confirmation through DNA barcode analysis. The East African specimens clustered with the western M. rosenbergii dacqueti subspecies in a phylogenetic analysis based on new and published mitochondrial 16S rRNA and cytochrome C oxidase subunit I (COI) sequences. Captured specimens spanned a size range of 110–310 mm total length and > 35% of females carried external eggs, implying that populations were established and self-sustaining. No active culture facilities or ponds with M. rosenbergii were found within the catchment. Nevertheless, the invasive populations supported a small-scale fishery that used bottom-set seine nets. The demonstrated presence of M. rosenbergii in at least two river systems, combined with the existence of favourable brackish water habitats for completing their life cycle, may indicate that river systems in East Africa are at a high risk of invasion by this species. Key information gaps for the region are highlighted.

The spiny lobster Panulirus homarus rubellus is endemic to the Southwest Indian Ocean, where it inhabits a narrow continental shelf between an exposed coast and the upper reaches of the strong western-boundary Agulhas Current. Long-lived phyllosoma larvae released in this dynamic ocean environment have an uncertain fate—they can be retained over the shelf by sub-mesoscale processes, dispersed downstream along the coast or across the Mozambique Channel, or become entrained in the Agulhas Current, and presumably lost. To assess gene flow and population genetic structure, we analyzed mitochondrial cytochrome oxidase subunit 1 and hypervariable control region sequences, and 19 nuclear microsatellite loci obtained from lobsters collected at nine sites in eastern South Africa, Mozambique and southeast Madagascar. Clustering analyses confirmed genetic connectivity among all populations, and gene flow patterns supported the hypothesis that nearshore processes, such as lee eddies and counter currents, retain some phyllosomas over the shelf; whereas, net gene flow direction was moderate towards the southwest. The Mozambique Channel did not impede contemporary gene flow from Madagascar to the African shelf, but return gene flow was rare. Different marker types showed contrasting gene flow patterns during contemporary and evolutionary periods, when Pleistocene glacial/interglacial cycles would have affected sea level, ocean currents and dispersal patterns. Despite genetic connectivity and the importance of local recruitment, recent gene flow suggests an ancillary source/sink dynamic concordant with the prevailing southwesterly direction of boundary currents at the shelf-edge—a factor to consider in regional fisheries and conservation strategies.

Full-length mitochondrial cytochrome c oxidase I (COI) sequence information from lobster phyllosoma larvae can be difficult to obtain when DNA is degraded or fragmented. Primers that amplify smaller fragments are also more useful in metabarcoding studies. In this study, we developed and tested a method to design a taxon-specific mini-barcode primer set for marine lobsters. The shortest, most informative portion of the COI gene region was identified in silico, and a DNA barcode gap analysis was performed to assess its reliability as species diagnostic marker. Primers were designed, and cross-species amplification success was tested on DNA extracted from a taxonomic range of spiny-, clawed-, slipper- and blind lobsters. The mini-barcode primers successfully amplified both adult and phyllosoma COI fragments, and were able to successfully delimit all species analyzed. Previously published universal primer sets were also tested and sometimes failed to amplify COI from phyllosoma samples. The newly designed taxon-specific mini-barcode primers will increase the success rate of species identification in bulk environmental samples and add to the growing DNA metabarcoding toolkit.

This study examines the fine‐scale population genetic structure and phylogeography of the spiny lobster Panulirus homarus in the Western Indian Ocean. A seascape genetics approach was used to relate the observed genetic structure based on 21 microsatellite loci to ocean circulation patterns, and to determine the influence of latitude, sea surface temperature (SST), and ocean turbidity (KD490) on population‐level processes. At a geospatial level, the genetic clusters recovered corresponded to three putative subspecies, P. h. rubellus from the SW Indian Ocean, P. h. megasculptus from the NW Indian Ocean, and P. h. homarus from the tropical region in‐between. Virtual passive Lagrangian particles advected using satellite‐derived ocean surface currents were used to simulate larval dispersal. In the SW Indian Ocean, the dispersion of particles tracked over a 4‐month period provided insight into a steep genetic gradient observed at the Delagoa Bight, which separates P. h. rubellus and P. h. homarus. South of the contact zone, particles were advected southwestwards by prevailing boundary currents or were retained in nearshore eddies close to release locations. Some particles released in southeast Madagascar dispersed across the Mozambique Channel and reached the African shelf. Dispersal was characterized by high seasonal and inter‐annual variability, and a large proportion of particles were dispersed far offshore and presumably lost. In the NW Indian Ocean, particles were retained within the Arabian Sea. Larval retention and self‐recruitment in the Arabian Sea could explain the recent genetic divergence between P. h. megasculptus and P. h. homarus. Geographic distance and minimum SST were significantly associated with genetic differentiation in multivariate analysis, suggesting that larval tolerance to SST plays a role in shaping the population structure of P. homarus.

Accurate species description in the marine environment is critical for estimating biodiversity and identifying genetically distinct stocks. Analysis of molecular data can potentially improve species delimitations because they are easily generated and independent, and yield consistent results with high statistical power. We used classical phylogenetic (maximum likelihood and Bayesian inference) and coalescent-based methods (divergence dating with fossil calibrations and coalescent-based species delimitation) to resolve the phylogeny of the spiny lobster Panulirus homarus subspecies complex in the Indo-West Pacific. Analyses of mitochondrial data and combined nuclear and mitochondrial data recovered Panulirus homarus homarus and Panulirus homarus rubellus as separately evolving lineages, while the nuclear data trees were unresolved. Divergence dating analysis also identified Panulirus homarus homarus and Panulirus homarus rubellus as two distinct clades which diverged from a common ancestor during the Oligocene, approximately 26 million years ago. Species delimitation using coalescent-based methods corroborated these findings. A long pelagic larval life stage and the influence of ocean currents on post-larval settlement patterns suggest that a parapatric mode of speciation drives evolution in this subspecies complex. In combination, the results indicate that Panulirus homarus rubellus from the Southwest Indian Ocean is a separately evolving lineage and possibly a separate species.