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.

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.

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.

Metabarcoding to determine the species composition and diversity of marine zooplankton communities is a fast‐developing field in which the standardization of methods is yet to be fully achieved. The selection of genetic markers and primer choice are particularly important because they substantially influence species detection rates and accuracy. Validation is therefore an important step in the design of metabarcoding protocols. We developed taxon‐specific mini‐barcode primers for the cytochrome c oxidase subunit I (COI) gene region and used an experimental approach to test species detection rates and primer accuracy of the newly designed primers for prawns, shrimps and crabs and published primers for marine lobsters and fish. Artificially assembled mock communities (with known species ratios) and unsorted coastal tow‐net zooplankton samples were sequenced and the detected species were compared with those seeded in mock communities to test detection rates. Taxon‐specific primers increased detection rates of target taxa compared with a universal primer set. Primer cocktails (multiple primer sets) significantly increased species detection rates compared with single primer pairs and could detect up to 100% of underrepresented target taxa in mock communities. Taxon‐specific primers recovered fewer false‐positive or false‐negative results than the universal primer. The methods used to design taxon‐specific mini‐barcodes and the experimental mock community validation protocols shown here can easily be applied to studies on other groups and will allow for a level of standardization among studies undertaken in different ecosystems or geographic locations.