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

• Main Author: Hull, Kelvin Lloyd
• Other Authors: Van der Merwe, Aletta, Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.
• Format: Thesis
• Language: English
• Published: Stellenbosch : Stellenbosch University 2018
• Subjects: Mustelus mustelus > Conservation; Population genetics; Mustelus > Genetics; Smoothhound sharks > Genome mapping; UCTD; Indian; North East Atlantic
• Online Access: http://hdl.handle.net/10019.1/105215

Thesis (MScAgric)--Stellenbosch University, 2018. 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 ...