Does the endangered Knysna seahorse, Hippocampus capensis, have a preference for aquatic vegetation type, cover or height?

The Knysna seahorse, Hippocampus capensis, is an endangered teleost confined to three South African estuaries. Its abundance within these systems is low and distributions are patchy. Consequently, monitoring population sizes is labour-intensive. The aim of this study was to establish if Knynsa seahorses are associated with specific regions within the estuaries, on which conservation efforts could concentrate. The relationship of Knysna seahorses with aquatic vegetation was analysed in the Knysna Estuary (the largest of the three estuarine systems inhabited by H. capensis) to determine whether this species shows a preference for a particular plant species, vegetation density or vegetation height. Seahorses were associated with five dominant aquatic plants: Zostera capensis, Caulerpa filiformis, Codium extricatum, Halophila ovalis and Ruppia cirrhosa. Together, these comprised 96% of the submerged objects with which seahorses were associated. The relative abundance of plant species changed along the estuary, but seahorses were present throughout the system, except at the estuary mouth, which was characterized by low plant densities and strong currents. No significant difference was found between the proportion of plant species present in a particular region of the estuary and the proportion of plants that seahorses used as holdfasts. However, when Z. capensis and C. filiformis were present at the same sites, adult seahorses preferred C. filiformis as holdfast. Adult seahorse density (individuals/m²) was significantly correlated with percentage vegetation cover and with holdfast length, but juvenile seahorse density was not. Nonetheless, significantly more adult and juvenile seahorses were found at sites characterized by high vegetation cover (>75%) than at sites with lower cover. Our results indicate that although there is some evidence that Knynsa seahorses prefer certain plant species over others, they are likely to be encountered anywhere in the estuary where aquatic plants are present. Conservation efforts in the Knysna Estuary should thus concentrate on such vegetated areas, which comprise approximately 11% of the total submerged surface area

Phylogeographic structure of Octopus vulgaris in South Africa revisited: identification of a second lineage near Durban harbor

In a previous study that investigated genetic structure of Octopus vulgaris along the South African coast by sequencing the mitochondrial cytochrome oxidase III gene (COIII), all sequences generated were identical. Such a finding is unusual, because mitochondrial DNA mutates quickly, and several marine invertebrates present in southern Africa show considerable genetic variation and structure. We reanalysed the samples using two different mitochondrial markers, namely cytochrome oxidase I (COI) and the large ribosomal subunit (16S rRNA). Sequences of both these markers showed variation. The conclusion of the previous study, that South Africa’s O. vulgaris population is characterised by a lack of genetic structure along the coast, is rejected. Some specimens from Durban (southeast Africa) were genetically more different from those found in the remainder of the country than were specimens from other regions (Tristan da Cunha and Senegal). We suggest that the lineage in Durban may have been recently introduced

A revision of the Pyura stolonifera species complex (Tunicata, Ascidiacea), with a description of a new species from Australia

Pyura stolonifera is a large solitary ascidian found in Africa, Australasia and South America. The taxonomic status of different populations of this species is disputed, especially since there is evidence for several distinct morphological and genetic units that point towards the existence of multiple cryptic species. While some researchers still recognize P. stolonifera as a single species, others treat the different populations as distinct species. Here, we present a revision of the P. stolonifera species complex based on the examination of samples from all regions where there are reliable reports of this taxon. We recognize four species that are both morphologically and genetically distinct, one of which is new to science and is formally described here. This species is morphologically distinct from the other three members of the species complex in terms of the colour and texture of the tunic, the arrangement of the gonads within the gut and the shape of the dorsal tubercle, among other characters. We name the new species Pyura dalbyi after Dr. J.E. Dalby Jr., whose research on its ecology and distribution provided the incentive for examining this species more closely

Mitochondrial DNA paradox: sex-specific genetic structure in a marine mussel despite maternal inheritance and passive dispersal

Background: When genetic structure is identified using mitochondrial DNA (mtDNA), but no structure is identified using biparentally-inherited nuclear DNA, the discordance is often attributed to differences in dispersal potential between the sexes. Results: We sampled the intertidal rocky shore mussel Perna perna in a South African bay and along the nearby open coast, and sequenced maternally-inherited mtDNA (there is no evidence for paternally-inherited mtDNA in this species) and a biparentally-inherited marker. By treating males and females as different populations, we identified significant genetic structure on the basis of mtDNA data in the females only. Conclusions: This is the first study to report sex-specific differences in genetic structure based on matrilineally-inherited mtDNA in a passively dispersing species that lacks social structure or sexual dimorphism. The observed pattern most likely stems from females being more vulnerable to selection in habitats from which they did not originate, which also manifests itself in a male-biased sex ratio. Our results have three important implications for the interpretation of population genetic data. First, even when mtDNA is inherited exclusively in the female line, it also contains information about males. For that reason, using it to identify sex-specific differences in genetic structure by contrasting it with biparentally-inherited markers is problematic. Second, the fact that sex-specific differences were found in a passively dispersing species in which sex-biased dispersal is unlikely highlights the fact that significant genetic structure is not necessarily a function of low dispersal potential or physical barriers. Third, even though mtDNA is typically used to study historical demographic processes, it also contains information about contemporary processes. Higher survival rates of males in non-native habitats can erase the genetic structure present in their mothers within a single generation

Signatures of seaway closures and founder dispersal in the phylogeny of a circumglobally distributed seahorse lineage

<p>Abstract</p> <p>Background</p> <p>The importance of vicariance events on the establishment of phylogeographic patterns in the marine environment is well documented, and generally accepted as an important cause of cladogenesis. Founder dispersal (i.e. long-distance dispersal followed by founder effect speciation) is also frequently invoked as a cause of genetic divergence among lineages, but its role has long been challenged by vicariance biogeographers. Founder dispersal is likely to be common in species that colonize remote habitats by means of rafting (e.g. seahorses), as long-distance dispersal events are likely to be rare and subsequent additional recruitment from the source habitat is unlikely. In the present study, the relative importance of vicariance and founder dispersal as causes of cladogenesis in a circumglobally distributed seahorse lineage was investigated using molecular dating. A phylogeny was reconstructed using sequence data from mitochondrial and nuclear markers, and the well-documented closure of the Central American seaway was used as a primary calibration point to test whether other bifurcations in the phylogeny could also have been the result of vicariance events. The feasibility of three other vicariance events was explored: a) the closure of the Indonesian Seaway, resulting in sister lineages associated with the Indian Ocean and West Pacific, respectively; b) the closure of the Tethyan Seaway, resulting in sister lineages associated with the Indo-Pacific and Atlantic Ocean, respectively, and c) continental break-up during the Mesozoic followed by spreading of the Atlantic Ocean, resulting in pairs of lineages with amphi-Atlantic distribution patterns.</p> <p>Results</p> <p>Comparisons of pairwise genetic distances among the seahorse species hypothesized to have diverged as a result of the closure of the Central American Seaway with those of published teleost sequences having the same distribution patterns show that the seahorses were among the last to diverge. This suggests that their cladogenesis was associated with the final closure of this seaway. Although two other divergence events in the phylogeny could potentially have arisen as a result of the closures of the Indonesian and Tethyan seaways, respectively, the timing of the majority of bifurcations in the phylogeny differed significantly from the dates of vicariance events suggested in the literature. Moreover, several divergence events that resulted in the same distribution patterns of lineages at different positions in the phylogeny did not occur contemporaneously. For that reason, they cannot be the result of the same vicariance events, a result that is independent of molecular dating.</p> <p>Conclusion</p> <p>Interpretations of the cladogenetic events in the seahorse phylogeny based purely on vicariance biogeographic hypotheses are problematic. We conclude that the evolution of the circumglobally distributed seahorse lineage was strongly influenced by founder dispersal, and suggest that this mode of speciation may be particularly important in marine organisms that lack a pelagic dispersal phase and instead disperse by means of rafting.</p

Is the Wild Coast in eastern South Africa a distinct marine bioregion?

Abstract: The South African coastline can be divided into at least four temperature-defined marine bioregions, including the tropical north-east coast, the subtropical east coast, the warm-temperate south coast, and the cool-temperate west coast. There are also two biogeographical transition zones, the south-west coast and the south-east 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

Oceanic dispersal barriers, adaptation and larval retention: an interdisciplinary assessment of potential factors maintaining a phylogeographic break between sister lineages of an African prawn

<p>Abstract</p> <p>Background</p> <p>Genetic breaks separating regional lineages of marine organisms with potentially high broadcasting abilities are generally attributed either to dispersal barriers such as currents or upwelling, or to behavioural strategies promoting self-recruitment. We investigated whether such patterns could potentially also be explained by adaptations to different environmental conditions by studying two morphologically distinguishable genetic lineages of the estuarine mudprawn <it>Upogebia africana </it>across a biogeographic disjunction in south-eastern Africa. The study area encompasses a transition between temperate and subtropical biotas, where the warm, southward-flowing Agulhas Current is deflected away from the coast, and its inshore edge is characterised by intermittent upwelling. To determine how this phylogeographic break is maintained, we estimated gene flow among populations in the region, tested for isolation by distance as an indication of larval retention, and reared larvae of the temperate and subtropical lineages at a range of different temperatures.</p> <p>Results</p> <p>Of four populations sampled, the two northernmost exclusively included the subtropical lineage, a central population had a mixture of both lineages, and the southernmost estuary had only haplotypes of the temperate lineage. No evidence was found for isolation by distance, and gene flow was bidirectional and of similar magnitude among adjacent populations. In both lineages, the optimum temperature for larval development was at about 23°C, but a clear difference was found at lower temperatures. While larvae of the temperate lineage could complete development at temperatures as low as 12°C, those of the subtropical lineage did not complete development below 17°C.</p> <p>Conclusion</p> <p>The results indicate that both southward dispersal of the subtropical lineage inshore of the Agulhas Current, and its establishment in the temperate province, may be limited primarily by low water temperatures. There is no evidence that the larvae of the temperate lineage would survive less well in the subtropical province than in their native habitat, and their exclusion from this region may be due to a combination of upwelling, short larval duration with limited dispersal potential near the coast, plus transport away from the coast of larvae that become entrained in the Agulhas Current. This study shows how methods from different fields of research (genetics, physiology, oceanography and morphology) can be combined to study phylogeographic patterns.</p

Climate change, genetics or human choice: why were the shells of mankind’s earliest ornament larger in the Pleistocene than in the Holocene?

The southern African tick shell, Nassarius kraussianus (Dunker, 1846), has been identified as being the earliest known ornamental object used by human beings. Shell beads dated from ~75,000 years ago (Pleistocene era) were found in a cave located on South Africa's south coast. Beads made from N. kraussianus shells have also been found in deposits in this region dating from the beginning of the Holocene era (<10,000 years ago). These younger shells were significantly smaller, a phenomenon that has been attributed to a change in human preference. We investigated two alternative hypotheses explaining the difference in shell size: a) N. kraussianus comprises at least two genetic lineages that differ in size; b) the difference in shell size is due to phenotypic plasticity and is a function of environmental conditions. To test these hypotheses, we first reconstructed the species' phylogeographic history, and second, we measured the shell sizes of extant individuals throughout South Africa. Although two genetic lineages were identified, the sharing of haplotypes between these suggests that there is no genetic basis for the size differences. Extant individuals from the cool temperate west coast had significantly larger shells than populations in the remainder of the country, suggesting that N. kraussianus grows to a larger size in colder water. The decrease in fossil shell size from Pleistocene to Holocene was likely due to increased temperatures as a result of climate change at the beginning of the present interglacial period. We hypothesise that the sizes of N. kraussianus fossil shells can therefore serve as indicators of the climatic conditions that were prevalent in a particular region at the time when they were deposited. Moreover, N. kraussianus could serve as a biomonitor to study the impacts of future climate change on coastal biota in southern Africa

The complete mitogenome of an undescribed clam shrimp of the genus Gondwanalimnadia (Branchiopoda: Spinicaudata), from a temporary wetland in Central District, Botswana

Clam shrimps (Spinicaudata) are a widespread and diverse crustacean group that frequent temporary aquatic habitats, but few complete mitochondrial genomes have been published for this group. Here, we report the mitogenome of an undescribed Gondwanalimnadia species from Botswana. Raw sequences were assembled into a single circular genome with a total length of 15,663 bp. Thirteen protein-coding genes, 22 tRNAs, and 2 rRNAs were identified using the MITOS pipeline. The mitogenome’s GC content is 33.52%. Phylogenetic analysis using protein-coding genes confirmed that Gondwanalimnadia sp. is closely related to another member of the Limnadiidae, Limnadia lenticularis

The complete mitogenome of the fairy shrimp Streptocephalus cafer (Lovén, 1847) (Crustacea: Branchiopoda: Anostraca) from an ephemeral pond in Botswana, southern Africa

Fairy shrimps (Anostraca) constitute an important component of seasonally aquatic habitats, but few complete mitochondrial genomes have been published for this group. Here, we report the mitogenome of a common southern African species, Streptocephalus cafer, from Botswana (accession number: MN720104). Low-coverage shotgun sequencing recovered two contigs 15653 bp and 1347 bp in length that are separated by a repetitive region of unknown length within the non-coding control region. The mitogenome’s GC content is 31.80%. Phylogenetic analysis using protein-coding genes confirms the sister taxon relationship of S. cafer with the only other congener whose mitogenome has been reconstructed to date, the Asian S. sirindhornae