Genetic variation within Cape stumpnose, Rhabdosargus holubi Steindachner (Teleostei: Sparidae)

Due to the nature of the marine environment genetic studies allow insight into behaviour and natural history that is difficult or impossible to identify by direct field observation. Current as well as historical population demography and gene flow can be detected by using molecular techniques. Genetic studies on only a few commercially important marine species along the South African coast have been conducted, although many marine fish species utilize estuaries as nursery areas and little attention has been afforded to studying larval distribution and recruitment of these species from a molecular point of view. Many of these estuarine associated species, especially in the South African milieu, are important for recreational and subsistence use. Associated with southern African estuaries are 13 species of the family Sparidae of which Cape stumpnose Rhabdosargus holubi is the most abundant. Juveniles are mostly confined to estuaries while the adults are strictly marine. Rhabdosargus holubi are serial spawners but temporally separated spawning peaks have been recorded along the South African coastline. Within the first part of this dissertation, the general characteristics of marine fish populations and the marine environment along the South African coast are being discussed. The main aim of this study was to determine the population genetic structure from estimates of nuclear and mitochondrial genetic variation across the distributional range of Rhabdosargus holubi. Samples were collected from 13 geographic localities along the South African coastline from St Lucia in the northeast to Klein River in the southwest. Juveniles were sampled in estuaries and adults were collected in the marine intertidal zone. Mitochondrial DNA control region fragments of 368 bp in length were obtained from a total of 214 individuals from all sampling localities. A total of 36 alleles were identified from 34 polymorphic sites. Following an allele homogeneity test, samples from different localities were lumped to represent six distinct geographical regions. Mitochondrial DNA control region analyses of juveniles showed high haplotype diversity and low nucleotide diversity with no divergent maternal lineages. No pattern between haplotype genealogy and geographic locality was evident. Population genetic analyses using heterologous microsatellite amplification have been successfully completed for a number of studies, including numerous studies of variation within marine fish species. Microsatellite studies have proven to be more sensitive in detecting subtle population structure than mtDNA and/or protein polymorphisms in high gene flow species. A total of 113 microsatellite loci previously isolated from phylogenetically closely related marine fish species were tested for amplification. The success rate of heterologous microsatellite amplification was extremely low (0.02%), with only two polymorphic loci amplifying consistently for analysing 133 individuals sampled from six localities along the distributional range of R. holubi. Results from these two loci were insufficient to draw conclusions about the population genetic structure of R. holubi along the South African coast. Possible reasons for the low rate of amplification success and future research recommendations are discussed. The findings from this study suggest that R. holubi is not geographically restricted, has high gene flow among localities and likely exist as a single stock.Dissertation (MSc (Genetics))--University of Pretoria, 2006.Geneticsunrestricte

Comparing DNA yield from fish scales following different extraction protocols

Studies on genetic diversity, adaptive potential and fitness of species have become a major tool in conservation biology. These studies require biological material containing a reliable source of DNA which can be extracted and analysed. Recently, non-invasive sampling has become the preferred sampling method of such biological material; particularly when studying endangered species. Elasmoid scales from teleost fish are an example of non-invasive samples from which DNA can successfully be extracted. This study compared different extraction protocols to find an optimal method for extracting DNA from teleost fish scales. This was done with the intent to use the protocol that yielded the highest quantity of DNA on dried, archived scales. The protocols tested in this study included (1) phenol/chloroform with a TNES-urea digestion bufer, (2) phenol/chloroform with an amniocyte digestion buffer and (3) Qiagen DNeasy Blood and Tissue Kit with variations in incubation times and temperatures of each protocol. While the phenol/chloroform with TNES-urea digestion buffer yielded significantly higher concentrations of DNA compared to the other protocols, all protocols followed in this study yielded sufficient quantities of DNA for further downstream applications. Therefore, while there are multiple viable options when selecting a DNA extraction protocol, each research project’s individual needs, requirements and resources need to be carefully considered in order to choose the most effective protocol.The National Research Foundation.https://www.nature.com/srepZoology and Entomolog

Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae : Murinae : Otomyini) : revision of the Otomys typus complex

We combined evidence from biogeography, craniodental traits, linear and geometric morphometrics (233 skulls), cytogenetics (karyotypes of 18 individuals) and mitochondrial DNA sequences (44 cytochrome b and 21 12S rRNA sequences) to test species limits within Otomys typus s.l. (Muridae: Murinae: Otomyini), a complex that is patchily distributed across alpine zones of Ethiopia and East Africa. Our results confirm the specific validity of O. dartmouthi, O. jacksoni, O. orestes, and O. uzungwensis, forms recently removed from synonymy under typus s.l.; support elevation of four other alpine forms to species (O. fortior, O. helleri, O. thomasi, and O. zinki); identify three additional new species (O. cheesmani sp. nov., O. simiensis sp. nov., O. yaldeni sp. nov.); and enable redefinition of O. typus s.s. as a species restricted to certain mountains west of the Great Rift Valley in Ethiopia (Simien and Guna Mountains in the north, extending to the highlands of the western rim of the Rift Valley). Phylogenetic interpretation of the cytochrome b data clearly demonstrates that the alpine morphotype once united under O. typus s.l. has originated independently at high elevations on several mountain ranges in eastern and northeastern Africa; although generally adapted to high-elevation vegetation, such alpine species are ecologically segregated from one another. Patterns of morphometric, genetic, and ecological differentiation among populations once misassigned to nominal O. tropicalis and O. typus more parsimoniously reflect regional cladogenesis along elevational gradients, rather than multiple, successive colonization by different ancestral forms from southern Africa as earlier supposed. Although incomplete and preliminary, information gathered for O. tropicalis indicates that it too is a species composite; several lines of research are discussed to redress its polyphyletic content. Our results, together with other recent taxonomic studies of Otomys, appreciably elevate the level of endemism within eastern Africa and underscore the significance of Africa's eastern highlands to the continental diversification of Otomyini.Nous avons combiné un ensemble de données, biogéographiques craniodentaires, morphométriques (linéaires et géométriques; 233 crânes), cytogénétiques (caryotypes de 18 individus) et moléculaires (ADN mitochondrial: 44 séquences de cytochrome b et 21 séquences de 12 rRNA) afin d’évaluer les délimitations d'espèces au sein d’Otomys typus s.l. (Muridae: Murinae: Otomyini), un complexe d’espèces distribué à travers les zones alpestres de l'Éthiopie et d'Afrique de l'Est. Nos résultats 1) confirment le statut spécifique d'O. dartmouthi, O. jacksoni, O. orestes et O. uzungwensis, des formes dont la synonymie avec typus s.l. a récemment été infirmée, 2) soutiennent l'élévation au statut d’espèce de quatre autres formes alpestres (O. fortior, O. helleri, O. thomasi et O. zinki), 3) permettent d’identifier trois nouvelles espèces supplémentaires (O. cheesmani sp. nov., O. simiensis sp. nov., O. yaldeni sp. nov.), et 4) nous permettent de redéfinir O. typus s.s. comme une espèce restreinte à certaines montagnes à l'ouest de la Vallée du Rift en Éthiopie (les montagnes Simien et Guna au nord, s'étendant aux pays montagneux du bord occidental de la vallée du Rift). L'interprétation phylogénétique des séquences de cytochrome b démontre clairement que la forme alpestre autrefois incluse dans O. typus s.l. est apparue de façon indépendante à de hautes altitudes sur plusieurs massifs montagneux en Afrique de l'Est et du Nord-Est. Bien que généralement adaptées à la végétation de haute altitude, de telles espèces alpestres sont écologiquement distinctes les unes des autres. Les différentiations morphométrique, génétique et écologique au sein des populations regroupées de façon incorrecte sous les noms O. tropicalis et O. typus reflètent plus parcimonieusement une diversification régionale suivant des gradients altitudinaux, plutôt qu’unecolonisation multiple, successive par différentes formes ancestrales d'Afrique du Sud, comme supposé antérieurement. Bien qu'incomplètes et préliminaires, les données obtenues pour O. tropicalis indiquent qu’il constitue aussi un complexe d'espèces. Plusieurs lignes de recherche sont envisagées afin de réévaluer son statut polyphylétique. Nos résultats, ajoutés à d'autres études taxinomiques récentes d'Otomys, élèvent sensiblement le niveau d'endémisme en l'Afrique de l'Est et soulignent l’importancedes hautes terres de l'est de l'Afrique dans la diversification continentale des Otomyini.We gratefully acknowledge the financial assistance of the Smithsonian Institution Short Term Visitor Award (in 2006), and a South African National Research Foundation Grant (between 2005 and 2007), which allowed P.J.T. to visit and study important North American and European museum collections of Otomys.http://www.mapress.com/zootaxa/nf201

Isolation and characterization of polymorphic tetranucleotide microsatellite loci in the pelagic perciform fish Pomatomus saltatrix (Linnaeus, 1766) from South Africa

Eight polymorphic microsatellite loci, containing simple tetranucleotide repeats, were isolated de novo from a Pomatomus saltatrix partial genomic library using the fast isolation by amplified fragment length polymorphism of sequences containing repeats protocol. These loci were further characterized in 100 individuals from two putative populations off the South African east coast. The loci are highly polymorphic with 18–37 alleles (on average 24 alleles/locus) and the observed heterozygosity in both populations was high (0.79). These loci will be used to assess population structuring in P. saltatrix along the southern African coast with consideration of implications for future management of this important linefish species

Evaluating the resolution power of new microsatellites for species identification and stock delimitation in the Cape hakes Merluccius paradoxus and Merluccius capensis (Teleostei : Merlucciidae)

The utility of 15 new and 17 previously published microsatellite markers was evaluated for species identification and stock delimitation in the deep-water hake Merluccius paradoxus and the shallow-water hake Merluccius capensis. A total of 14 microsatellites was polymorphic in M. paradoxus and 10 in M. capensis. Two markers could individually discriminate the species using Bayesian clustering methods and a statistical power analysis showed that the set of markers for each species is likely to detect subtle genetic differentiation (FST < 0.006), which will be valuable to delimit and characterise genetic stocks.BCLME/BENEFIT and the Department of Science and Technology African Coelacanth Ecosystem Programme (ACEP) II.University of Pretoria’s postdoctoral programme.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1095-86492016-05-31hb201