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.

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.

Scleractinia of the Maputaland reef complex (MRC) in South Africa exist at the margins of the Western Indian Ocean (WIO) coral distribution and are the only substantial hermatypic coral communities in South Africa. Pocillopora species occupy a conspicuous component of the MRC, and previous investigations identified three species of Pocillopora utilizing conventional taxonomy. Thus, our aims were four-fold: to elucidate Pocillopora species diversity using genetic techniques, primarily using species delimitation methods based on the ORF gene; to test for the presence of hybridisation within the Pocillopora community on the South-West margin of distribution in the Indian Ocean using two nuclear and two mitochondrial markers; to test the presence of cryptic species, using 13 microsatellite markers, finally, to elucidate the degree of genetic diversity within each Pocillopora species found and compare this to communities in lower latitudes. We illustrate taxonomic inconsistencies between these inventories and our phylogenetic data. The MRC harbours unique populations of Pocillopora , consisting of three species hypothetically co-occurring throughout the south WIO, namely: P . meandrina / P . eydouxi , commonly misidentified as P . verrucosa , P . verrucosa , sometimes correctly identified, but also commonly misidentified as P . damicornis sensu lato , and P . villosa , almost always misidentified as P . eydouxi . The hypothesis that hybrid swarms of Pocillopora occur in marginal environments such as the MRC was not supported, with low levels of introgressive hybridization reported instead. Analyses illustrate low genetic diversity at the species and population resolutions, suggesting a small founder population for each species. Nevertheless, these populations are demographically unique, exhibiting high levels of ITS2 haplotype endemism compared to higher latitude populations and the rest of the WIO. Pocillopora diversity on the MRC represents a unique assemblage and warrants further protection.

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