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.

Intraspecific genetic structure in widely distributed marine species often mirrors the boundaries between temperature-defined bioregions. This suggests that the same thermal gradients that maintain distinct species assemblages also drive the evolution of new biodiversity. Ecological speciation scenarios are often invoked to explain such patterns, but the fact that adaptation is usually only identified when phylogenetic splits are already evident makes it impossible to rule out the alternative scenario of allopatric speciation with subsequent adaptation. We integrated large-scale genomic and environmental datasets along one of the world's best-defined marine thermal gradients (the South African coastline) to test the hypothesis that incipient ecological speciation is a result of divergence linked to the thermal environment. We identified temperature-associated gene regions in a coastal fish species that is spatially homogeneous throughout several temperature-defined biogeographic regions based on selectively neutral markers. Based on these gene regions, the species is divided into geographically distinct regional populations. Importantly, the ranges of these populations are delimited by the same ecological boundaries that define distinct infraspecific genetic lineages in co-distributed marine species, and biogeographic disjunctions in species assemblages. Our results indicate that temperature-mediated selection represents an early stage of marine ecological speciation in coastal regions that lack physical dispersal barriers.

The New Zealand fur seal (Arctocephalus forsteri) passed through a population bottleneck due to commercial sealing during the eighteenth to nineteenth centuries. To facilitate future management options, we reconstructed the demographic history of New Zealand fur seals in a Bayesian framework using maternally inherited, mitochondrial DNA sequences. Mitogenomic data suggested two separate clades (most recent common ancestor 5000 years ago) of New Zealand fur seals that survived large-scale human harvest. Mitochondrial haplotype diversity was high, with 45 singletons identified from 46 individuals although mean nucleotide diversity was low (0.012 ± 0.0061). Variation was not constrained geographically. Analyses of mitogenomes support the hypothesis for a population bottleneck approximately 35 generations ago, which coincides with the peak of commercial sealing. Mitogenomic data are consistent with a pre-human effective population size of approximately 30,000 that first declined to around 10,000 (due to the impact of Polynesian colonization, particularly in the first 100 years of their arrival into New Zealand), and then to 100-200 breeding individuals during peak of commercial sealing.

The South African coastline can be divided into at least four temperature-defined marine bioregions, including the tropical northeast coast, the subtropical east coast, the warm-temperate south coast, and the cool-temperate west coast. There are also two biogeographical transition zones, the southwest coast and the southeast coast (or Wild Coast). The former is sometimes considered a distinct marine bioregion, but no such status has yet been suggested for the Wild Coast. Previous data on the distribution of a recently described but very common coastal crab, Hymenosoma longicrure, indicated that this species could be a Wild Coast endemic. If confirmed, this would be a first indication that this region harbours unique fauna, and that additional research is required to determine whether the Wild Coast constitutes a distinct bioregion that needs to be managed separately from other coastal regions. In the present study, we generated novel genetic data for H. longicrure and compared the species' range with that of its southern African congeners. We found that H. longicrure occurs north of the Wild Coast, where its range overlaps with that of H. projectum. This finding rejects the idea that the Wild Coast harbours endemic fauna and suggests that the ranges of the two species may be linked to the subtropical and tropical bioregions, respectively, with some southward dispersal facilitated by the southward-flowing Agulhas Current. We conclude that there is as yet no compelling evidence that the Wild Coast is a distinct marine bioregion, and concur with previous biogeographical studies which have suggested that the Wild Coast is an area in which species from the subtropical and warm-temperate bioregions have overlapping ranges. Nonetheless, that fact that no biological information is available for the majority of the region's estuaries highlights the necessity of comprehensively documenting the biodiversity of this understudied region to fully resolve this issue.