Mitochondrial genome assembly and population genetics of the common smoothhound shark, Mustelus mustelus

Hull, Kelvin Lloyd (2018-11)

Thesis (MScAgric)--Stellenbosch University, 2018.

Thesis

ENGLISH ABSTRACT: Knowledge of evolutionary history and population genetic structuring in economically important marine species are integral factors for a more comprehensive fisheries management approach in order to preserve regional and global biodiversity. The common smoothhound, Mustelus mustelus, is a vulnerable species of shark overexploited by numerous fisheries across its wide-spread distribution range, from the Mediterranean Sea and north-east Atlantic to the south-west Indian Ocean. Although previous studies have assessed the genetic diversity and population structure along the South African coast, genetic resources are scarce, and little is known about the genetic variation across its wider distribution. This study aimed to assemble and annotate the complete mitochondrial genome of the species from available next-generation sequencing data, and assess historical and contemporary patterns of genetic diversity and population structure across three ocean basins, using a 571 bp fragment of the non-coding mitochondrial control region (mtCR) and nine species-specific microsatellite markers. The complete mitogenome of M. mustelus and the phylogenetic reconstruction of two other mitogenomes for the genus illustrated a closer relationship with the placental M. griseus, and validated the previously hypothesised correlation of reproductive mode with the phylogenetic placement within the Mustelus genus. Furthermore, the mtCR displayed higher levels of variability in comparison to other species assessed in the Carcharhiniformes order, and was therefore considered a suitable marker to be utilised in conjunction with nuclear markers to assess intraspecific patterns of diversity and structure on a global scale. Overall, M. mustelus was characterised by low to moderate genetic diversity (h = 0.867; ℼ = 0.00437; AR = 2.5, HE = 0.375), with the Mediterranean populations appearing to exhibit the lowest mitochondrial diversity (h = 0.443; ℼ = 0.00083), while the southern north-east Atlantic populations displayed the lowest nuclear diversity (AR = 2.6, HE = 0.325). For the mtCR sequences, a total of 18 haplotypes, and two main haplogroups representing the northern and southern hemispheres, were identified (mean h = 0.861; mean π = 0.0042), with a high degree of population divergence (ΦST = 0.658, P < 0.01). The microsatellite analyses including F-statistics (FST: 0.070 – 0.556, P < 0.01), multivariate and Bayesian clustering confirmed genetic differentiation between the three ocean regions investigated, with finer scale population structure in each ocean basin. No correlation between genetic and geographical distance was observed (R2 = 0.0034, P = 0.415), however this was most likely due to the inclusion of island populations and a stepping stone model of connectivity between collections. In conclusion, a cautious approach to the management of the species should be taken, as some regions appear to have a degree of connectivity despite being significantly differentiated. In areas with limited fisheries data, finer-scale analyses should be performed in order to develop a more comprehensive management strategy to conserve this threatened species.

AFRIKAANSE OPSOMMING: Kennis van die evolusionêre geskiedenis en populasie genetiese struktuur van ekonomiese belangrike mariene spesies is belangrike faktore vir 'n meer omvattende benadering tot visserybestuur met die doel om plaaslike en globale biodiversiteit te behou. Die hondhaai, Mustelus mustelus, is 'n kwesbare haai spesie wat oorbenut word deur baie visserye oor hul verspreidingsgebied wat strek vanaf die Mediterreense See en die noordoostelike Atlantiese Oseaan tot die suidwes Indiese Oseaan. Alhoewel vorige studies die genetiese diversiteit en populasie struktuur langs die Suid-Afrikaanse kus ondersoek het is genetiese hulpbronne skaars vir hierdie spesie, en min inligting is beskikbaar rakende die genetiese variasie vir M. mustelus. Hierdie studie het daarom gepoog om beskikbare hoë deurset volgordebepalings data te gebruik om die volledige mitokondriale genoom van die spesie te bepaal en te annoteer. Historiese en hedendaagse patrone van genetiese diversiteit en populasie struktuur oor drie oseaanbekkens was geevalueer, met die gebruik van 'n 571 bp fragment van die nie-koderende mitokondriale beheerstreek (mtBS) en nege spesies-spesifieke mikrosatelliet merkers. Die volledige mitogenoom van M. mustelus en die filogenetiese rekonstruksie met twee ander mitogenome vir die genus het 'n nader verwantskap met die plasentale M. griseus geïllustreer en die vorige hipotetiese korrelasie van reproduktiewe modus met die filogenetiese plasing binne die Mustelus genus bevestig. Die mtBS het hoër vlakke van variasie in die Carcharhiniformes orde vertoon, en is daarom beskou as 'n geskikte merker om gebruik te word in samewerking met nukleêre merkers om intraspesifieke patrone van diversiteit en struktuur op ‘n wêreldwye skaal te evalueer. ‘n Lae tot matige genetiese diversiteit (h = 0.867; π = 0.00437; AR = 2.5, HE = 0.375) was waargeneem, met die Mediterreense populasies met die laagste mitokondriale diversiteit (h = 0.443; π = 0.00083), terwyl die suidelike noordoostelike Atlantiese populasies die laagste nukleêre diversiteit (AR = 2.6, HE = 0.325) gehad het. Die mtBS belyning het bestaan uit 'n totaal van 18 haplotipes en twee kern haplogroepe, wat die noordelike en suidelike hemisfeer respektiewelik verteenwoordig (gemiddelde h = 0.861; gemiddelde π = 0.0042), met 'n hoë graad van populasie differensiasie (ΦST = 0.658, P < 0,01). Die mikrosatelliet analises wat F-statistieke (FST: 0.070 - 0.556, P <0.01), multivariate en Bayesiese groepering ingesluit het, het bevestig dat genetiese differensiasie tussen die drie oseaan gebiede bestaan, met fyner populasie struktuur in elke oseaanbekken. Geen korrelasie tussen genetiese en geografiese afstand was waargeneem nie (R2 = 0.0034, P = 0.415), maar dit was waarskynlik as gevolg van die eiland populasies wat ingesluit was en 'n “stepping-stone” model van konnektiwiteit tussen die steekproef populasies. 'n Versigtige benadering vir die bestuur van die spesie moet aangewend word, aangesien sommige gebiede gedeeltelik verbind is, alhoewel daar ‘n aansienlike hoeveelheid differensiasie is. In gebiede met beperkte vissery data moet fyner skaal studies uitgevoer word om 'n meer omvattende bestuurstrategie te ontwikkel met die doel om hierdie bedreigde spesies te bewaar.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/105215
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