Molecular species identification and spatio-temporal assessment of genetic diversity in the smooth hammerhead shark Sphyrna zygaena in South Africa

Kuguru, Gibbs (2017-03)

Thesis (MSc)--Stellenbosch University, 2017.

Thesis

ENGLISH ABSTRACT: The South African coast hosts a unique oceanographic regime with an enriched habitat able to support a diverse biota of chondrichthyans (sharks, skates, rays and chimaeras). Investigating these species and populations on a molecular level could aid in conserving this rich chondrichthyan biodiversity. As a precursor, a case study regarding the composition of species in three different South African fisheries was evaluated to determine the utility of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene in delimiting species identity. Through this, a number of issues surrounding misidentification and cryptic speciation were recognized, and the efficacy of CO1 was tested and proved to be useful in identifying chondrichthyans affected in South African fisheries. One of these species, the smooth hammerhead shark (Sphyrna zygaena) displays a high degree of site fidelity to Mossel Bay as evidenced by the rise in the number of neonate and juvenile hammerheads during the summer season. This species is vulnerable as they are in danger of overfishing and the destruction of their natural habitat. With a low fecundity and a long generational time, recovery of near-depleted populations is prolonged. In this study mitochondrial sequence data and microsatellite markers were used to assess genetic diversity within and between S. zygaena sampling cohorts collected from Mossel Bay to the KwaZulu Natal coast. Additionally, kinship between the juvenile individuals was determined and parental genotypes were reconstructed from the neonate and juvenile smooth hammerhead sharks sampled in the Mossel Bay area. Significant population subdivision was evident between individuals sampled in the warm temperate south coast (Mosselbay) and the subtropical east coast (Algoa Bay and KwaZulu Natal), with asymmetric gene flow mainly from the south to the east coast. Highly significant population differentiation was seen between sampling years, indicative of differential temporal stocks utilizing Mossel Bay each year. Analysis of kinship revealed a high degree of sibling relationships within and between seasons, which is likely due to an overlap of some parental genotypes across seasons. The results obtained here can assist with decisions regarding the conservation of chondrichthyan biodiversity in South Africa while it is also recommended that genetic structure and temporal variation of S. zygaena populations be evaluated on a finer scale in the future.

AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse kus huisves 'n unieke oseanografiese gebied wat 'n diverse biota van ‘chondrichthyan’ spesies (haaie, rôe, pylsterte en chimaeras) ondersteun. Molekulêre ondersoeke van hierdie spesies en populasies kan bydrae tot die bewaring van hierdie ryk chondrichthyan biodiversiteit. ʼn Gevallestudie is gedoen met betrekking tot die samestelling van spesies in drie verskillende Suid-Afrikaanse visserye om die bruikbaarheid van die mitokondriale sitochroom oksidase subeenheid 1 (SO1) geen te evalueer vir spesies identifisering. Dit het aanleiding gegee tot 'n aantal kwessies rondom die misidentifikasie en kriptiese spesiasie in visserye. Die doeltreffendheid van die SO1 geen is ook bevestig vir die identifisering van ‘chondrichthyans’ geaffekteer in Suid-Afrikaanse visserye. Een van hierdie spesies, die gladde hammerkop haai (Sphyrna zygaena) vertoon 'n hoë mate van affiniteit aan Mosselbaai soos blyk uit die toename in die aantal jong hammerkop haaie in die somer seisoen. Hierdie spesie is kwesbaar as gevolg van oorbenutting in visserye asook die vernietiging van hul natuurlike habitat. Met 'n lae vrugbaarheid en 'n lang generasie tyd, kan herstel van geaffekteerde populasies aansienlik verleng word. In hierdie studie is mitokondriale DNS volgorde data en mikrosatelliet merkers gebruik om genetiese diversiteit binne en tussen S. zygaena individue gekollekteer van Mosselbaai tot die KwaZulu Natal kus te evalueer. Daarbenewens is die verwantskap tussen die jong individue bereken asook die ouerlike genotipes gerekonstrueer vanaf die jong gladde hammerkop haaie vanaf Mosselbaai. Beduidende populasie struktuur is tussen individue waargeneem afkomstig vanaf die warm gematigde suidkus (Mosselbaai) en die subtropiese ooskus (Algoabaai en KwaZulu-Natal), met asimmetriese geenvloei hoofsaaklik van die suide tot die ooskus. Hoogs beduidende populasie verskille is waargeneem tussen die twee seisoene, wat ‘n aanduiding kan wees van twee verskillende populasies wat Mosselbaai elke jaar besoek. Verwantskap analise het 'n hoë mate van verwantskappe tussen sibbe gewys binne en tussen seisoene, en kan waarskynlik as gevolg van 'n oorvleueling van sommige ouer genotipes oor seisoene wees. Die resultate wat in hierdie studie verkry is, kan help met die verdere besluitneming rakende die bewaring van mariene biodiversiteit in Suid-Afrika. Dit word wel aanbeveel dat die genetiese struktuur en temporale variasie van S.zygaena populasies waargeneem in hierdie studie geëvalueer word op 'n fyner skaal in die toekoms.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/101154
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