Description of a new montane freshwater crab (Arthropoda, Malacostraca, Decapoda, Potamonautidae) from the Eastern Cape, South Africa.

A new species of freshwater crab, Potamonautesamatholesp. nov., is described from the Winterberg-Amathole mountain range in the Eastern Cape Province, South Africa. Morphologically, P.amathole Peer & Gouws, sp. nov. most closely resembles P.tuerkayi but can be distinguished by key morphological characters including the variation in the shape of the subterminal segment of gonopod 2 between both species. Genetically, P.amathole Peer & Gouws, sp. nov. is placed within the clade of small-bodied, mountain-dwelling crabs including P.parvispina, P.parvicorpus, P.brincki, P.tuerkayi, P.baziya, and P.depressus. The new species is found in slow-moving mountain streams and pools at high altitudes. The continued discovery and description of new freshwater crab species reinforces the need for ongoing research, especially in under-sampled regions.

Resurrection of Lethrinus scoparius Gilchrist amp; Thompson, 1908 (Perciformes: Lethrinidae), from South African waters.

Lethrinus nebulosus (Forsskl, 1775) is distributed throughout the Indian Ocean, Indonesia and the West-central Pacific. Given recent evidence suggesting two cryptic species of L. nebulosus in the southwestern Indian Ocean, we implemented a multispecies coalescent approach using nuclear and mitochondrial DNA loci and conducted Bayesian tests of species delimitation. One population extends from southern Mozambique to Kenya, and the other from northern KwaZulu-Natal (South Africa) southwards, with a zone of overlap between them. This study confirms that the South African population can be identified as a separate species, previously identified as Lethrinus scoparius Gilchrist Thompson, 1908, and can be distinguished from L. nebulosus by live and fresh colouration and with genetic data, but not consistently by morphometric or meristic parameters, other than in preorbital length cf. head length. Lethrinus scoparius is resurrected and redescribed herein.

Upeneus floros, a new goatfish from South Africa and Mozambique, with updated taxonomic accounts for U. guttatus and U. pori and a key to Western Indian Ocean Upeneus species (Mullidae).

The highly diverse goatfish genus Upeneus (Mullidae) requires enhanced attention regarding the possible occurrence of undescribed species in insufficiently explored regions. This study focuses on the South-Western Indian Ocean region (SWIO), and on the so-called japonicus-group, a taxonomic species group of Upeneus. Based on in-situ observations and collections in Sodwana Bay, KwaZulu-Natal, South Africa, the Floros goatfish, U. floros n. sp., is described. Detailed comparative studies of colour patterns and morphological characters of all other 13 japonicus-group species were undertaken as well as COI barcoding. The new species occurs in the coastal area between Angoche, N Mozambique and KwaZulu-Natal and partly overlaps in distribution with two similar species, U. guttatus, widely distributed in the Indo-W Pacific, and U. saiab, assumed to be endemic in a small area off Angoche. Two additional japonicus-group species occurring in the SWIO, U. seychellensis from the Seychelles Bank and U. pori from the Mediterranean Sea (as Lessepsian migrant), Northern Red Sea and Madagascar, were also compared. Because specimens as well as in-situ photographs of U. floros have been erroneously identified as either U. guttatus or U. pori during previous studies, updated taxonomic accounts and diagnoses are provided for these species taking size-related and population differences into account. For U. pori, of which a single preserved specimen from SW Madagascar was known so far, a new record from NE Madagascar is reported based on three specimens and a fresh-colour photo. Upeneus floros can be distinguished from U. guttatus and U. pori by a combination of three characters: head length, first dorsal-fin height and number of gill rakers. Upeneus guttatus can be distinguished from the other two species by disproportionally higher anterior dorsal-fin spines vs. a proportional decrease of dorsal-fin spines in height, barbels mostly yellow vs. white or creamy-white, and slightly fewer pectoral-fin rays. COI barcoding detected a clear distinction between U. guttatus and U. floros and U. pori, respectively, but no significant divergence between the two latter species. COI barcoding also failed to differentiate several other Upeneus species which are clearly distinguished morphologically. Possible interrelationships between species distribution patterns and physical oceanography are discussed. An identification key for the 22 WIO Upeneus species is provided.

A taxonomic revision of Gymnothorax undulatus (Anguilliformes: Muraenidae) in the Western Indian Ocean, with description of a new species.

The taxonomic status of the widely distributed Indo-Pacific undulated moray eel, Gymnothorax undulatus, is revised using morphological and genetics features. Ninety-seven specimens previously identified as G. undulatus were examined and their mitochondrial COI and 16S rRNA genes were analysed. The multivariate analysis of eight morphometric characters resulted in separation with little to no overlap among some geographic regions. These groupings explained more than 90% of the total variation, with 86.6% overall classification. Two color morphs were identified, and the South African population was described as new species, Gymnothorax elaineheemstrae n. sp., distinct from G. undulatus in having mottled and faintly reticulated color pattern, 134-136 total vertebrae and further confirmed by the genetic analysis of COI and 16S rRNA with > 0.1 genetic distance. The morphological and genetics results indicate that G. undulatus, previously treated as a single species, consists of more than one species.

Evidence of genetic differentiation in cigar wrasse Cheilio inermis (Labridae) within the western Indian Ocean.

Patterns of genetic structure and connectivity of the monotypic cigar wrasse Cheilio inermis within western Indian Ocean (WIO) are poorly understood. Whether the species exists as a single panmictic population across the WIO is unclear. Sequence data were generated from two mitochondrial genes (cytochrome b and ATPase 6) and one nuclear intron (S7 intron I). High levels of haplotype and allelic diversity (h = 0.88-0.98; A = 0.95-0.98), along with low nucleotide diversities were observed across all markers. The pairwise ΦST values indicated differentiation of Tanga from the four WIO localities (Inhaca, Nosy Bé, Gazi, and Shimoni), as well as differentiation between the northernmost WIO localities. AMOVAs indicated high differentiation among defined locality groups, whereas nuclear gene analysis found little differentiation among groups. The observed genetic differentiation in C. inermis could be caused by oceanic barriers, and by limited larval dispersal with the pelagic larvae possibly settling near their parental origin and promoting differentiation.

A new species of Nemipterus (Pisces: Nemipteridae) from the Western Indian Ocean.

A new species of threadfin bream, Nemipterus elaine, from the Western Indian Ocean is described. The new species is known so far only from off the coast of southern Mozambique, and appears most closely related morphologically and genetically to N. randalli Russell, 1986, but differs in having shorter pectoral and pelvic fins, and the upper caudal lobe produced to form a short, bright yellow filament (a long red trailing filament present in N. randalli). A key to the species of Nemipterus in the Western Indian Ocean is provided.

Molecular and morphological evidence reveals hybridisation between two endemic cyprinid fishes.

The geographic occurrence of moggel Labeo umbratus × mud fish Labeo capensis hybrids and the threat of hybridisation to the genetic integrity of L. umbratus were investigated. Genetic evidence from mtDNA cytb and nDNA s7 intron sequence data indicated probable interspecific hybridisation in two impoundments, Hardap Dam (Orange River Basin, Namibia) and Darlington Dam (Sundays River Basin, Eastern Cape, South Africa). Some putative hybrids were morphologically identifiable on account of their meristic and morphometric intermediacy to the parent species. Human activities appear to drive the observed hybridisation, either through dam construction and direct stocking of L. umbratus or via translocation of Labeo capensis and the previously isolated Orange River lineage of L. umbratus into the southern-flowing systems by inter-basin water transfers. It is recommended that further translocation of fish from these areas should be avoided.

Mating System, Reproductive Success, and Sexual Selection in Bluntnose Klipfishes (Clinus cottoides).

A critical part of the sexual selection process in animals is the genetic mating system. Quantifying mating systems, especially in species with cryptic life histories can be challenging. One approach is to use genotypic markers and accurate parentage analysis, along with methods to account for bias when sampling natural populations, to calculate sexual selection metrics derived from Bateman's principles. In this study, 3 microsatellites were used to genotype 48 adults (23 female and 25 male) and 342 offspring from known mothers of live-bearing bluntnose klipfish. Parentage analysis was performed to interpret mating and reproductive success for both sexes. Metrics quantified were the opportunity for selection (I), the opportunity for sexual selection (Is), absolute (ßss), and standardized (ß'ss) Bateman gradients and the maximum intensity of precopulatory sexual selection (s'max). Multiple mating by both sexes were revealed by parentage analysis. However, females did not show significant Bateman gradients or a significant maximum intensity of precopulatory sexual selection (s'max), whereas male sexual selection metrics were all significantly greater than 0. These results suggest a polygynandrous mating system for this species. There is an opportunity for sexual selection to act on males but not females in this population, which is evolutionary tied to anisogamy, parental investment, and sex roles.

Cryptic lineages in the Wolf Cardinalfish living in sympatry on remote coral atolls.

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.

MicroCT imaging applied to description of a new species of Pagurus Fabricius, 1775 (Crustacea: Decapoda: Anomura: Paguridae), with selection of three-dimensional type data.

A new species of hermit crab, Pagurus fraserorum n. sp. (family Paguridae) is described from rocky subtidal reefs off KwaZulu-Natal, South Africa, and illustrated using both conventional drawings and colour photographs, and via three-dimensional (3D) X-ray micro-computed tomography (µCT). Because of the limitation µCT has in detecting very fine and soft structures, a novel approach of manually drawing setation and spinulation onto the two-dimensional images of the 3D visualizations was used to illustrate the pereopods. In addition, an interactive figure and rotation movie clips in the supplement section complement the species description, and the 3D raw data of the 3D type data are downloadable from the Gigascience Database repository. The new species is the sixth species of Pagurus Fabricius, 1775 reported from South Africa and is closely allied to the Indo-Pacific P. boriaustraliensis Morgen, 1990 and P. pitagsaleei McLaughlin, 2002, from which it differs by its shorter ocular peduncles, by the armature of the carpus of the right cheliped, and also in colouration. This study presents the first description of a hermit crab in which a majority of taxonomic details are illustrated through 3D volume-rendered illustrations. In addition, colour photographs and COI molecular barcodes are provided, and the latter compared to COI sequences of specimens from Western Australia previously identified as P. boriaustraliensis and of specimens of P. pitagsaleei from Taiwan, as well as to three additional South African members of the genus. The South African taxon was confirmed to be genetically distinct from all species tested.

The taxonomic status of the South African straptail, Macruronus capensis Davies, 1950 (Pisces, Gadiformes, Macruronidae).

The first record of the straptail fish, genus Macruronus, from South Africa was based on a single specimen captured off the Atlantic Cape coast and described as a new species, M. capensis Davies 1950. Davies did not examine specimens of the other extant nominal species in the genus, but based his conclusions solely on references to the original descriptions of M. novaezelandiae (Hector 1870) and M. magellanicus Lönnberg 1907. We show that all of the characters used by Davies (1950) to distinguish M. capensis from its congeners are in fact shared by the other nominal species of this genus. We also present molecular evidence from a Macruronus specimen recently caught off South Africa to support the conclusion that M. capensis is a junior synonym of M. novaezelandiae.

Cryptic species and parallel genetic structuring in Lethrinid fish: Implications for conservation and management in the southwest Indian Ocean.

Analysis of genetic variation can provide insights into ecological and evolutionary diversification which, for commercially harvested species, can also be relevant to the implementation of spatial management strategies and sustainability. In comparison with other marine biodiversity hot spots, there has been less genetic research on the fauna of the southwest Indian Ocean (SWIO). This is epitomized by the lack of information for lethrinid fish, which support socioeconomically important fisheries in the region. This study combines comparative phylogeographic and population genetic analyses with ecological niche modeling to investigate historical and contemporary population dynamics of two species of emperor fish (Lethrinus mahsena and Lethrinus harak) across the SWIO. Both species shared similarly shallow phylogeographic patterns and modeled historical (LGM) habitat occupancies. For both species, allele frequency and kinship analyses of microsatellite variation revealed highly significant structure with no clear geographical pattern and nonrandom genetic relatedness among individuals within samples. The genetic patterns for both species indicate recurrent processes within the region that prevent genetic mixing, at least on timescales of interest to fishery managers, and the potential roles of recruitment variability and population isolation are discussed in light of biological and environmental information. This consistency in both historical and recurrent population processes indicates that the use of model species may be valuable in management initiatives with finite resources to predict population structure, at least in cases wherein biogeographic and ecological differences between taxa are minimized. Paradoxically, mtDNA sequencing and microsatellite analysis of samples from the Seychelles revealed a potential cryptic species occurring in sympatry with, and seemingly morphologically identical to, L. mahsena. BLAST results point to the likely misidentification of species and incongruence between voucher specimens, DNA barcodes, and taxonomy within the group, which highlights the utility and necessity of genetic approaches to characterize baseline biodiversity in the region before such model-based methods are employed.

Redescription of Potamonautes sidneyi (Rathbun, 1904) (Decapoda, Potamonautidae) and description of a new congeneric species from KwaZulu-Natal, South Africa.

A new species of freshwater crab, Potamonautes danielsisp. n., is described from the southern region of the KwaZulu-Natal Province, South Africa. Potamonautes danielsi most closely resembles Potamonautes sidneyi which is re-described here, but can be distinguished by a suite of key morphological characters including carapace shape and width, slim pereopods, inflated propodi of the chelipeds, and the shape and terminal segment length:subterminal segment length ratio of the 1st gonopod. In a previous study (Gouws et al. 2015), a 9.2-11.8 % divergence was found in the mitochondrial COI and 16S genes of the Potamonautes sidneyi clade, allowing for the delineation of a new species. Despite the clear molecular distinction between the two species, it is difficult to separate them based on individual morphological characters, as there is a great deal of overlap even among key features. The new species is found in slow-moving mountain streams and pools at high altitudes between Umhlanga and Mtamvuna, in KwaZulu-Natal.

Description of a new species of Potamonautes MacLeay, 1838, from the iSimangaliso Wetland Park, South Africa.

A new species of freshwater crab, Potamonautesisimangaliso sp. n., is described from the western shores of False Bay, Hluhluwe, within the iSimangaliso Wetland Park, South Africa. While bearing a superficial resemblance to Potamonauteslividus, the new species has been found to be genetically distinct, diverging from the former by 7.4-7.8% in mtDNA. Potamonautesisimangaliso most closely resembles Potamonauteslividus, but is distinguished by a unique suite of carapace characters, colouration, and size. The new species also lives in close association with oxygen-poor, fresh ephemeral pans, while the habitat of Potamonauteslividus is well above the surface water line of the closest water body. An updated identification key for the Potamonautes species of South Africa is provided.

A new species of the cardinalfish genus Siphamia (Perciformes, Apogonidae) from West Papua, Indonesia.

A new species of the cardinalfish genus Siphamia is described from specimens collected in the Province of West Papua, Indonesia, at depths of 50-72 m. Siphamia papuensis n. sp. has a striated light organ which makes it a member of the S. tubifer species group. Within this group it is closely related to S. argentea, sharing with the latter 13 pectoral-fin rays, 9 developed gill rakers and an irregular pattern of yellowish green bars on the body. It differs from S. argentea in having an incomplete lateral line and in lacking dark marks on the head, and at the origin and end of the dorsal-fin and anal-fin bases, as well as the absence of red spots along the light organ and along the back. Japanese records of S. tubulata are reidentified as S. argentea, and new locality records for S. argentea and S. stenotes are reported. Analysis of sequence data from a 16S rDNA fragment revealed the clear separation of S. papuensis n. sp., S. argentea and other included Siphamia species (S. jebbi, S. tubifer and S. stenotes). 

Evolutionary drivers of diversification and distribution of a southern temperate stream fish assemblage: testing the role of historical isolation and spatial range expansion.

This study used phylogenetic analyses of mitochondrial cytochrome b sequences to investigate genetic diversity within three broadly co-distributed freshwater fish genera (Galaxias, Pseudobarbus and Sandelia) to shed some light on the processes that promoted lineage diversification and shaped geographical distribution patterns. A total of 205 sequences of Galaxias, 177 sequences of Pseudobarbus and 98 sequences of Sandelia from 146 localities across nine river systems in the south-western Cape Floristic Region (South Africa) were used. The data were analysed using phylogenetic and haplotype network methods and divergence times for the clades retrieved were estimated using *BEAST. Nine extremely divergent (3.5-25.3%) lineages were found within Galaxias. Similarly, deep phylogeographic divergence was evident within Pseudobarbus, with four markedly distinct (3.8-10.0%) phylogroups identified. Sandelia had two deeply divergent (5.5-5.9%) lineages, but seven minor lineages with strong geographical congruence were also identified. The Miocene-Pliocene major sea-level transgression and the resultant isolation of populations in upland refugia appear to have driven widespread allopatric divergence within the three genera. Subsequent coalescence of rivers during the Pleistocene major sea-level regression as well as intermittent drainage connections during wet periods are proposed to have facilitated range expansion of lineages that currently occur across isolated river systems. The high degree of genetic differentiation recovered from the present and previous studies suggest that freshwater fish diversity within the south-western CFR may be vastly underestimated, and taxonomic revisions are required.

Re-description of two species of the cardinalfish genus Archamia (Teleostei: Apogonidae) from the Red Sea and Western Indian Ocean.

The cardinalfishes Archamia bilineata and A. pallida were originally described from a small number of specimens collected in the Gulf of Aqaba, Red Sea and Oman, respectively. Both species are re-described using specimens collected recently in Yemen and Kenya, including the first known adult of A. pallida. These new collections increased the geographical range of both species considerably. Differences between the two populations now known for each of the species are discussed.

Lack of taxonomic differentiation in an apparently widespread freshwater isopod morphotype (Phreatoicidea: Mesamphisopidae: Mesamphisopus) from South Africa.

The unambiguous identification of phreatoicidean isopods occurring in the mountainous southwestern region of South Africa is problematic, as the most recent key is based on morphological characters showing continuous variation among two species: Mesamphisopus abbreviatus and M. depressus. This study uses variation at 12 allozyme loci, phylogenetic analyses of 600 bp of a COI (cytochrome c oxidase subunit I) mtDNA fragment and morphometric comparisons to determine whether 15 populations are conspecific, and, if not, to elucidate their evolutionary relationships. Molecular evidence suggested that the most easterly population, collected from the Tsitsikamma Forest, was representative of a yet undescribed species. Patterns of differentiation and evolutionary relationships among the remaining populations were unrelated to geographic proximity or drainage system. Patterns of isolation by distance were also absent. An apparent disparity among the extent of genetic differentiation was also revealed by the two molecular marker sets. Mitochondrial sequence divergences among individuals were comparable to currently recognized intraspecific divergences. Surprisingly, nuclear markers revealed more extensive differentiation, more characteristic of interspecific divergences. This disparity and the mosaic pattern of differentiation may be driven by stochastic population crashes and genetic bottlenecks (caused by seasonal habitat fluctuations), coupled with genetic drift.

Phylogenetic relationships of the southern African freshwater crab fauna (Decapoda: Potamonautidae: Potamonautes) derived from multiple data sets reveal biogeographic patterning.

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.