Species identification and comparative population genetics of four coastal houndsharks based on novel NGS‐mined microsatellites

Abstract

The common smooth-hound (Mustelus mustelus) is the topmost bio-economically and recreationally important shark species in southern Africa, western Africa, and Mediterranean Sea. Here, we used the Illumina HiSeq™ 2000 next-generation sequencing (NGS) technology to develop novel microsatellite markers for Mustelus mustelus. Two microsatellite multiplex panels were constructed from 11 polymorphic loci and characterized in two populations of Mustelus mustelus representative of its South African distribution. The markers were then tested for cross-species utility in Galeorhinus galeus, Mustelus palumbes, and Triakis megalopterus, three other demersal coastal sharks also subjected to recreational and/or commercial fishery pressures in South Africa. We assessed genetic diversity (N A , A R , H O , H E, and PIC) and differentiation (F ST and D est ) for each species and also examined the potential use of these markers in species assignment. In each of the four species, all 11 microsatellites were variable with up to a mean N A of 8, A R up to 7.5, H E and PIC as high as 0.842. We were able to reject genetic homogeneity for all species investigated here except for T. megalopterus. We found that the panel of the microsatellite markers developed in this study could discriminate between the study species, particularly for those that are morphologically very similar. Our study provides molecular tools to address ecological and evolutionary questions vital to the conservation and management of these locally and globally exploited shark species. K E Y W O R D Scross-amplification, Galeorhinus galeus, Illumina sequencing, microsatellites, Mustelus mustelus, Mustelus palumbes, Triakis megalopterus | INTRODUCTIONSharks play a crucial role in maintaining the ecological balance in marine ecosystems as keystone species, yet these animals are gradually declining worldwide in seascapes heavily impacted by humans (Dulvy et al., 2014). Such declines in wild populations not only will have negative ecological impacts on lower trophic species (Price, O'Bryhim, Jones, & Lance, 2015) but can also alter the levels and distribution of | 1463genetic diversity among populations (Dudgeon et al., 2012). It is likely that sharks may not respond well to population declines compared to other marine fishes owing to their K-selected life-history traits, i.e., slow growth, late maturity, and low reproductive outputs (Compagno, 1984;Ebert, Fowler, Compagno, & Dando, 2013). This highlights the need for conservation and management measures to ensure the sustainable utilization of these fishery resources. Implementing such measures often requires information on fishery dynamics, biological and baseline ecological data which in most cases are not yet available (Velez-Zuazo, Alfaro-Shigueto, Mangel, Papa, & Agnarsson, 2015).Molecular approaches have been very useful in providing insight into historical and contemporary demography of various commercially important shark species, especially with respect to population connectivity, stock structure, and m...

Population genetics of Southern Hemisphere tope shark (Galeorhinus galeus): Intercontinental divergence and constrained gene flow at different geographical scales

“…galeus were predicted to occur as a result of habitat preference [ 23 ] and could therefore also be linked to the bioregions found along the South African coastline. More recently, Maduna et al, 2017 [ 84 ] also implicated the Cape Agulhas boundary as the main barrier to gene flow in four coastal shark species including G . galeus .…”

Evidence for sperm storage in common smoothhound shark Mustelus mustelus and paternity assessment in a single litter from South Africa

“…Individuals were genotyped using two microsatellite multiplex panels; five species‐specific loci (Mmu‐1, Mmu‐3, Mmu‐7, Mmu‐8 and Mmu‐11) and six cross‐amplified microsatellite loci (Mca‐B6, Mca‐B22, Gg‐2, Gg‐22 and Gg‐23) with PCR amplifications performed as outlined in Maduna et al . () and Rossouw et al . (), respectively (Table ).…”

“…Baseline allele frequencies were obtained for each microsatellite multiplex panel from a population data set consisting of 48 adult M. mustelus collected from the south‐west Indian Ocean given the interoceanic population genetic structure determined for common smoothhound (Maduna et al ., ; ). All loci were evaluated for scoring errors and allelic dropout using Micro‐Checker 2·2·3 (van Oosterhout et al, ).…”

Microsatellite development and detection of admixture among three sympatric Haploblepharus species (Carcharhiniformes: Scyliorhinidae)

“…Furthermore, owing to highly conserved microsatellite flanking sequences (Martin, Pardini, Noble, & Jones, 2002), cross-species amplification has been demonstrated in chondrichthyans with relatively high success rates (Blower, Corley, Hereward, Riginos, & Ovenden, 2015;Griffiths et al, 2011). The use of cross-amplified markers in a standardized panel has proven valuable for molecular species identification and comparative population genetics (Giresi et al, 2015;Maduna et al, 2017;Marino et al, 2015).…”