A phylogeny of South African east coast intertidal rocky-shore Polychaete worms (Annelida) and the genetic structure and demographic history of an example, Marphysa corallina.

Master of Science in Biology. University of KwaZulu-Natal, Westville 2015.The Annelida is an evolutionarily ancient invertebrate taxon. Recent studies have found that the formerly described sister taxon of the Polychaeta, Clitellata, is a derived Polychaete group thus making Polychaeta a paraphyletic group. Polychaete worms represent one of the most diverse invertebrate groups and are well represented in a variety of environments such as temporary freshwater puddles, rocky intertidal shores, estuaries and the abyssal plain. Polychaetes are fundamentally important in their environments as many are regarded as ecosystem engineers. Phylogenetic relationships within the Polychaeta are poorly understood and some species level classifications are uncertain due to the large number of polychaete worms present. In Chapter two, the phylogenetic relationships within the commonly found polychaete families (Nereididae and Eunicidae) were analysed using the universal mitochondrial cytochrome oxidase subunit 1 (COI). Within Eunicidae, analyses supported a polyphyletic Marphysa and Eunice which is consistent with previous results as individuals from both genera are nested among one another. Within Nereididae, relationships between genera and species were poorly supported and complex. Genera did not form exclusive clades but instead grouped with one another. A large degree of homoplasy has been recorded for the family which could have attributed to the convoluted groupings. Thus it has been suggested that genera from both Eunicidae and Nereididae be revised. Marphysa corallina is a poorly studied Eunicid polychaete which has a tropical indo-west distribution. It was observed to be a common worm among others on the intertidal rocky shores of KwaZulu-Natal and the Eastern Cape. In Chapter three, the population genetic structure and demographic history of M. corallina was investigated using two genes: universal mitochondrial cytochrome oxidase subunit 1 (COI) and the nuclear intron spacer region (ITS1). Diagnostic taxonomic characters were used to identify and validate the specimens as Marphysa corallina. The COI marker revealed that populations were highly connected to one another and formed a large panmictic population whereas ITS1 showed shallow genetic structuring of populations. Family Eunicidae individuals are known to lack a long lived planktonic larval stage which could not have contributed to panmixia as demostrated by the COI marker. Demographic results indicated that populations had recently undergone sudden expansions which could have falsely resembled highly connected populations. Estimation of divergence times places the expansions in the mid to late Pleistocene. Populations had not reached migration-drift equilibrium thus contemporary population distributions of Marphysa corallina along the east coast of South Africa are largely shaped by past climatic events such as in the Pleistocene

Taxonomic and molecular assessment of the apparently alien and cosmopolitan Nereididae Blainville, 1818 polychaetes from South Africa

Thesis (PhD)--Stellenbosch University, 2019.ENGLISH ABSTRACT: Polychaete worms provide many ecosystem services and are useful indicator species. Some are invasive and may threaten biodiversity and ocean economies. However, the convoluted taxonomic history of polychaetes has led to incorrect classifications of indigenous and alien species as they are commonly mistaken for cosmopolitan species. Thus, species with a dubious taxonomic status are termed pseudocosmopolitan species. Three such species, Pseudonereis variegata Grube, 1857, Platynereis dumerilii Audouin & Milne Edwards, 1833 and Platynereis australis Schmarda, 1861 were prioritised for investigation owing to their alien or cryptogenic status elsewhere, multiple synonymised names, globally disjunct distribution and a widespread South African distribution. The first overarching aim of this thesis was to determine whether these three species are indigenous or alien to South Africa or harbour cryptic and new species. Thorough morphological revisions and molecular datasets (mtCOI and nDNA) revealed that all three species are indigenous to South Africa. The local Pseudonereis podocirra n. comb. (Schmarda, 1861) was incorrectly synonymised as P. variegata (type locality: Chile) and Platynereis B sp. nov. was misidentified as P. dumerilii (type locality: Mediterranean). Individuals identified as P. australis (type locality: New Zealand) represent P. massiliensis (Moquin-Tandon, 1869) (type locality: Mediterranean), but since individuals from Italy and Portugal nested within the South African clade and had comparatively low genetic diversities, this species is likely indigenous to South Africa and alien in the Mediterranean. However, because P. massiliensis is part of a cryptic species complex in the Mediterranean, its name is considered doubtful and hence is referred to as P. massiliensis s.l. Pseudonereis podocirra’s wrongful synonymisation was due to poor species descriptions and conservative taxonomic views whereas misidentifications of the two Platynereis species was because they are truly cryptic. These results together with the finding that ~50% of other local nereidids may be pseudocosmopolitan, indicate that diversity of nereidids has been underestimated. Short-term solutions are proposed when dealing with pseudocosmopolitan polychaete species and recommendations are made regarding the clarification of P. massiliensis s.l. in the Mediterranean, the molecular identification of the global Platynereis species complex and taxonomic revisions of P. variegata from Chile. The second overarching aim was to determine factors contributing to the phylogeographic structure of these three sympatric South African species to determine the underlying factors driving their present-day distributions. Using mtCOI, P. massiliensis s.l. displayed three geographically structured lineages separated by the Cape Point and Cape Agulhas phylogeographic breaks whereas Platynereis B sp. nov. showed two well-mixed regional lineages separated by the Cape Agulhas break. In contrast, nDNA demonstrated well-mixed populations for both species and the intrinsic properties of each marker was used to explain the differences in patterns. Pseudonereis podocirra exhibited a panmictic meta-population using a mitochondrial dataset which persisted even when using a high-throughput SNP dataset. Age, hence resilience, were likely factors contributing to the contrasting patterns of structure and connectivity as P. podocirra n. comb. was demonstrated to be an evolutionarily older species. Fluctuating temperatures and paleo-conditions during the Pleistocene probably resulted in the southeastern expansions of all three species while radiations along the west coast were inferred for Platynereis B sp. nov. and P. podocirra. Platynereis B sp. nov. and P. massiliensis s.l. speciated sympatrically due to reproductive isolation and temperature, whereas P. massiliensis s.l. and P. dumerilii are hypothesised to have speciated allopatrically. All Platynereis species display evidence of morphological stasis despite their ancient divergence times. Pseudonereis podocirra and P. variegata (Chile) speciated allopatrically and have undergone morphological stasis or convergence. Historical climatic oscillations, oceanographic currents, ecoregions and larval development were factors contributing to the phylogeographic structure whilst allopatry and sympatry coupled with morphological stasis were identified as the most likely mode and mechanism of cryptic speciation of these species in South Africa.AFRIKAANSE OPSOMMING: Borselwurms verteenwoordig ‘n groot deel van seebodem habitat diversiteit en verskaf vele ekosisteem dienste insluitend voedingstof hersirkulasie en habitat voorsiening. Baie is indringer-spesies en kan die plaaslike diversiteit en mariene-ekonomie bedreig. Bygesê, die ingewikkelde taksonomiese geskiedenis van borselwurms het gelei tot die inkorrekte klassifikasie van inheemse en indringer spesies deur hul as wydverspreide of kosmopolitiese spesies te klassifiseer. Dus, spesies met ‘n twyfelagtige taksonomiese status word pseudo-komopolitaanse spesies genoem. Drie sulke spesies, Pseudonereis variegata Grube, 1857, Platynereis dumerilii Audouin & Milne Edwards, 1833 en Platynereis australis Schmarda, 1861 is as prioriteit beskou vir verdere ondersoek namate hul status as indringer-, twyfelagtige- of kriptogeniese- spesies elders, asook verskeie sinonomiese name, gebroke globale verspreiding en wydverspreide Suid-Afrikaanse verspreiding. Die eerste oorkoepelende doelwit was om vas te stel of hierdie Suid-Afrikaanse spesies wel inheems tot die streek is. Deeglike morfologiese wysigings en molekulêre datastelle (mtCOI en nDNS) het al drie spesies as inheems openbaar. Die plaaslike Pseudonereis podocirra n. comb. (Schmarda, 1861) is inkorrek as sinoniem van P. variegata (tipe ligging: Chile) aangedui en Platynereis B sp. nov. was verkeerdelik identifiseer as P. dumerilii (tipe ligging: Mediterreens). Individue identifiseer as P. australis (tipe ligging: Nieu-Seeland) verteenwoordig P. massiliensis (Moquin-Tandon, 1869) (tipe ligging: Mediterreens), maar sedert individue van Italië en Portugal geneste is binne die Suid-Afrikaanse klade en vergelykend lae genetiese diversiteit gehad het is daar tot die gevolgtrekking gekom dat hierdie spesie inheems tot Suid-Afrika is en ‘n indringer spesie in die Mediterreense see is. Omdat P. massiliensis deel vorm van n kriptiese spesie-kompleks in die Mediterreense see word die naam as twyfelagtig beskou en word dus voortaan verwys na “P. massiliensis”. Die verkeerdelike sinonomie van Pseudonereis podocirra was as gevolg van onvoldoende spesie beskryfwings asook die konservatiewe uitsigte van taksonomiese kenners terwyl die verkeerdelike identifikasie van die twee Platynereis spesies plaasgevind het as gevolg van hul kriptiese morfologie. Hierdie resultate tesame met die vinding dat ~50% van ander plaaslike nereidid spesies pseudo-kosmopolitaans kan wees is beduidend daarop dat die diversiteit van nereidid speies onderskat is. Kort-termyn oplossings word voorgestel vir die hantering van pseudo-kosmopolitaanse spesies en aanbevelings word gemaak met betrekking tot die klassifikasie van “P. massiliensis” in die Mediterreense see, die molekulêre identifikasie van die globale Platynereis spesie kompleks en taksonomiese wysigings van P. variegate van Chile. Die tweede oorkoepelende doelwit was om vas te stel watter faktore bydrae tot die filo-geografiese strukture van die drie simpatriese Suid-Afrikaanse spesies om sodoende die onderliggende faktore wat hedendaagse verspreiding dryf vas te stel. Met mtCOI het “P. massiliensis” drie geografies gestruktureerde bevolkings gehad wat geskei is by die Kaapse Punt en Kaap Agullhas filo-geoagrafiese breuke terwyl Platynereis B sp. nov. net twee goed gemengde plaaslike afstammelinge aandui wat geskei is by die Kaap Agullhas breuk. In kontras het die nDNS goed gemengde bevolkings aangedui vir beide spesies en die intrinsieke eieskappe van elke merker is gebruik om die verskille in patrone te verduidelik. Pseudonereis podocirra het ‘n panmitiese meta-bevolking aangedui met ‘n mitochondriese daastel en die is volhou selfs na die gebruik van ‘n hoë-deurset ENP datastel. Ouderdom, en dus veerkragtigheid, was waarskynlik faktore wat bygedra het tot die kontrasterende patrone van struktuur en verbinding aangesien P. podocirra n. comb. demonstreer is as die ouer evolusionêre spesie. Wisselende temperature en paleo-toestande gedurende die Pleistoseen het waarskynlik gelei tot die suidoosterse uitbreidings van al drie spesies terwyl uitbreidings na die weskus net afgelei is vir Platynereis B sp. nov. en P. podocirra. Platynereis B sp. nov. en “P. massiliensis” het simpatriese spesiasie ondergaan as gevolg van reproduktiewe isolasie en temperatuur terwyl “P. massiliensis” en P. dumerilii waarskynlik allopatriese spesiasie ondergaan het. Alle Platynereis spesies toon bewyse van morfologiese stase ten spyte van hul antieke afwykingstye. Pseudonereis podocirra en P. variegata (Chile) het allopatriese spesiasie ondergaan en het morfologoese stase of konvergensie ondergaan. Historiese klimaat wisselinge, oseografiese strome, eko-streke en larwe ontwikkeling was faktore wat bygedra het tot die filo-geografiese struktuur terwyl allopatrie en simpatrie gekoppel met morfologiese stase identifiseer is as die mees waarskynlike modus en meganisme van kriptiese spesiasie van hierdie spesies in Suid-Afrika.Ph

Redescriptions of Neanthes Kinberg, 1865 (Annelida: Errantia: Nereididae) species from worldwide regions

The present study redescribes four species of Neanthes Kinberg, 1865 (Nereididae de Blainville, 1818) based on their type specimens collected from different worldwide localities: Neanthes chilkaensis (Southern, 1921) from India, N. galetae (Fauchald, 1977) from Panama, N. helenae (Kinberg, 1865) from St Helena Island, and N. mossambica (Day, 1957) from Mozambique. The morphology of the types was re-examined for the first time after the species were originally described, and incorporated the recent improvements in the standards and terminology for describing nereidid features. The arrangement of paragnaths on area VI stood out among the diagnostic features used to distinguish these four species. Neanthes chilkaensis and N. helenae are the unique nereidids bearing p-bar paragnaths on the area VI. Both species are also distinctive as the former species only exhibited p-bar paragnaths on the area VII–VIII and the latter ventrolateral projections on the apodous segment. Further examination revealed that N. nanciae (Day, 1949) from St Helena is a junior synonym of N. helenae. Moreover, N. galetae and N. mossambica are distinguishable from other species also by the development of dorsal cirri, neuropodial postchaetal lobe and ventral ligule, the presence/absence of merged paragnaths on area IV, paired oesophageal caeca, among other features. This study has further contributed to the morphological delimitation of the species in Neanthes as a first step towards revising the genus

A closer look at the taxonomic and genetic diversity of endemic South African Marphysa Quatrefages, 1865

The current study investigates the final unresolved cosmopolitan species of Marphysa in South Africa, Marphysa corallina, collected from KwaZulu Natal, Eastern and Western Cape provinces, together with another species collected from northern KwaZulu Natal. Morphological and genetic data prove that M. corallina, originally described from Hawaii, does not occur in South Africa. The curvature of the inner base on maxilla I, the elevated inner base of maxilla II, and the ventral cirrus as a transverse welt with a rounded tip allow us to identify it as a new species of Treadwellphysa, T. izinqa sp. nov. (common name: brown wonderworm). Characteristic traits include the basal reddish and distal golden colour of the subacicular hook, the ear-shaped postchaetal lobe, and tridentate falcigers which is reported for the first time for the genus. This species is harvested as bait on the south coast of SA, although less frequently than the more common blood wonderworm, Marphysa haemasona Quatrefages, 1866, and can be distinguished by its more uniform brown colouration and white-tipped antennae. A second species, Marphysa mzingazia sp. nov., is characterized by red eyes, six branchial filaments extending to the posterior end, the golden aciculae in posterior chaetigers, weakly bidentate yellow/brown subacicular hooks, and the presence of similar sized spinigers along the body. A molecular analysis based on cytochrome oxidase I fragments confirm both taxa as different species. A key for all South African species of Marphysa is included

Confirmation of the southern African distribution of the marine sponge Hymeniacidon perlevis (Montagu, 1814) in the context of its global dispersal

Background Intertidal rocky shore surveys along the South African coastline (∼3,000 km) have demonstrated the presence and abundance of the encrusting orange sponge Hymeniacidon perlevis (Montagu, 1814), a well-known globally distributed species. After analysing the southern African populations, we gained a better understanding of the genetic structure of this now-accepted global species. Apart from confirming the presence of a single population of H. perlevis, we also determined its distribution in the southern African intertidal rocky shore ecosystem, compared its genetic diversity to congeners, predict its global distribution via environmental niche modelling, and discussed possible underlying mechanisms controlling the species’ global distribution. Methods We surveyed the South African coastline and sampled sponges at 53 rocky shore sites spanning over 3,000 km, from Grosse Bucht south of Lüderitz (Namibia) to Kosi Bay on the east coast of South Africa. DNA sequences of the nuclear rDNA internal transcribed spacer (ITS1) and the COI mitochondrial gene were obtained from 61 samples and compared them to a world-wide sample of other H. perlevis sequences. Using environmental predictor variables from the global dataset BIO-ORACLE, we predicted the probability of global occurrence of the species using an ensemble of eight distribution models. Results South African specimens were found to be 99–100% identical to other populations of H. perlevis (=H. sinapium) from other world-wide regions. The presence of a single population of H. perlevis in southern Africa is supported by genetic data, extending its distribution to a relatively wide geographical range spanning more than 4,000 km along the temperate southern African coast. The predicted global occurrence by ensemble model matched well with the observed distribution. Surface temperature mean and range were the most important predictor variables. Conclusion While H. perlevis appears to have been introduced in many parts of the world, its origins in Europe and southern Africa are unclear