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Epinephelus andersoni is a range-restricted species that is endemic to the south-east coast of Africa from Quissico in Mozambique to Knysna in South Africa. The species is an important commercial and recreational linefish species that is currently considered to be optimally exploited although there have been some signs of depletion within its range. This is likely because of its complex life-history including diandric protogyny and high residency, which make it potentially vulnerable to over-exploitation. This study analysed the genetic structure and diversity of E. andersoni using nuclear (intron 1 S7) and mitochondrial (cyt b) DNA genes for 240 and 269 individuals,respectively, to provide information for fisheries conservation and management. S7-1 allelic diversity was high (0.801) with the AMOVA showing significantly high among group variation (ΦCT = 0.204, p

Coral reef health and biodiversity is under threat worldwide due to rapid climate change. However, much of the inter- and intra-specific diversity of coral reefs are undescribed even in well studied taxa such as fish. Delimiting previously unrecognised diversity is important for understanding the processes that generate and sustain biodiversity in coral reef ecosystems and informing strategies for their conservation and management. Many taxa that inhabit geographically isolated coral reefs rely on self-recruitment for population persistence, providing the opportunity for the evolution of unique genetic lineages through divergent selection and reproductive isolation. Many such lineages in corals and fish are morphologically similar or indistinguishable. Here, we report the discovery and characterisation of cryptic lineages of the Wolf Cardinalfish, Cheilodipterus artus, from the coral atolls of northwest Australia using multiple molecular markers from mitochondrial (CO1 and D-loop) and nuclear (microsatellites) DNA. Concordant results from all markers identified two highly divergent lineages that are morphologically cryptic and reproductively isolated. These lineages co-occurred at daytime resting sites, but the relative abundance of each lineage was strongly correlated with wave exposure. It appears, therefore, that fish from each lineage are better adapted to different microhabitats. Such cryptic and ecologically based diversity appears to be common in these atolls and may well aid resilience of these systems. Our results also highlight that underwater surveys based on visual identification clearly underestimate biodiversity, and that a taxonomic revision of the Cheilodipterus genus is necessary.

The obligate, freshwater isopod suborder Phreatoicidea is represented in South Africa by ten species contained within the endemic genus Mesamphisopus (Mesamphisopidae). Here, phylogenetic hypotheses are proposed to describe the evolutionary and biogeographic history of the genus with respect to drainage basin evolution and to assess species diversity, particularly among populations variably identified as Mesamphisopus abbreviatus or Mesamphisopus depressus . Twenty-three ingroup taxa were examined, including eight known species and representatives of the M. abbreviatus – depressus complex. Allozyme data from 12 loci were analysed phenetically and cladistically. Mitochondrial DNA sequence data from the 12S ribosomal RNA and cytochrome c oxidase subunit I genes were analysed as a combined mtDNA data set and as a total data set in combination with recoded allele frequency data. Analyses retrieved (1) a monophyletic Mesamphisopus ; (2) Mesamphisopus tsitsikamma and a Mesamphisopus paludosus + Mesamphisopus penicillatus clade as basal lineages; (3) a Mesamphisopus capensis + Mesamphisopus baccatus clade; and (4) a clade containing the M. abbreviatus – depressus complex, with these taxa nested among several other species. Large genetic distances among taxa and the paraphyly of the members of the M. abbreviatus – depressus complex suggested the presence of hidden taxonomic diversity in Mesamphisopus . Clear biogeographic patterns emerged with lineages and clades mostly restricted to geographically discrete regions. Patterns showed remarkable similarity to those seen in the region’s terrestrial fauna and bore no relation to the history of drainage basins. These patterns suggested that vicariance and, possibly, limited dispersal events played a major role in the evolution of Mesamphisopus .

The phylogenetic relationships among the southern African freshwater crab species were examined using partial sequence data from three mitochondrial genes (12S rRNA, 16S rRNA, and mtDNA COI) 26 morphological characters and 14 allozyme loci. The aims of the present study were firstly to determine whether freshwater crab species that live in the same geographic region share a close phylogenetic relationship. Secondly, to investigate whether hybridizing species are genetically closely related and thirdly, to test for the validity of subgenera based on the genetic data sets. Phylogenetic analysis based on sequence data revealed largely congruent tree topologies and some associations had consistently high bootstrap support, and these data did not support Bott's subgeneric divisions. The morphological data were less informative for phylogenetic reconstruction while the allozyme data generally supported patterns recovered by the sequence data. A combined analysis of all the data recovered two monophyletic clades, one comprised of small-bodied mountain stream species and the other clade consisting of large-bodied riverine species. The combined analyses reflected clear biogeographic patterning for these river crabs. In addition, there was a clear correlation between genetic distance values and the ability of sympatric species to hybridize.