When two oceans meet: regional population genetics of an exploited coastal shark, Mustelus mustelus

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...

Section: Discussionsupporting

confidence: 93%

Section: Discussionsupporting

confidence: 90%

Section: Discussionsupporting

confidence: 81%

Section: Discussionsupporting

confidence: 77%

supporting

confidence: 92%

See 3 more Smart Citations

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

Maduna

Rossouw

Silva³

et al. 2017

Addressing the complex phylogenetic relationship of the Gempylidae fishes using mitogenome data

Mthethwa

Merwe

Roodt‐Wilding

2023

The Gempylidae (snake mackerels) family, belonging to the order Perciformes, consists of about 24 species described in 16 genera primarily distributed in tropical, subtropical, and temperate seas worldwide. Despite substantial research on this family utilizing morphological and molecular approaches, taxonomy categorization in this group has remained puzzling for decades prompting the need for further investigation into the underlying evolutionary history among the gempylids using molecular tools. In this study, we assembled eight complete novel mitochondrial genomes for five Gempylidae species (Neoepinnula minetomai, Neoepinnula orientalis, Rexea antefurcata, Rexea prometheoides, and Thyrsites atun) using Ion Torrent sequencing to supplement publicly available mitogenome data for gempylids. Using Bayesian inference and maximum-likelihood tree search methods, we investigated the evolutionary relationships of 17 Gempylidae species using mitogenome data. In addition, we estimated divergence times for extant gempylids. We identified two major clades that formed approximately 48.05 (35.89-52.04) million years ago: Gempylidae 1 (Thyrsites atun, Promethichthys prometheus, Nealotus tripes, Diplospinus multistriatus, Paradiplospinus antarcticus, Rexea antefurcata, Rexea nakamurai, Rexea prometheoides, Rexea solandri, Thyrsitoides marleyi, Gempylus serpens, and Nesiarchus nasutus) and Gempylidae 2 (Lepidocybium flavobrunneum, Ruvettus pretiosus, Neoepinnula minetomai, Neoepinnula orientalis, and Epinnula magistralis). The present study demonstrated the superior performance of complete mitogenome data compared with individual genes in phylogenetic reconstruction. By including T. atun individuals from different regions, we demonstrated the potential for the application of mitogenomes in species phylogeography.

Seascape Genomics of the Smooth Hammerhead Shark Sphyrna zygaena Reveals Regional Adaptive Clinal Variation

Grobler,

Klein,

Dicken

et al. 2024

Globally, hammerhead sharks have experienced severe declines owing to continued overexploitation and anthropogenic change. The smooth hammerhead shark Sphyrna zygaena remains understudied compared to other members of the family Sphyrnidae. Despite its vulnerable status, a comprehensive understanding of its genetic landscape remains lacking in many regions worldwide. The present study aimed to conduct a fine‐scale genomic assessment of Sphyrna zygaena within the highly dynamic marine environment of South Africa's coastline, using thousands of single nucleotide polymorphisms (SNPs) derived from restriction site‐associated DNA sequencing (3RAD). A combination of differentiation‐based outlier detection methods and genotype‐environment association (GEA) analysis was employed in Sphyrna zygaena. Subsequent assessments of putatively adaptive loci revealed a distinctive south to east genetic cline. Among these, notable correlations between adaptive variation and sea‐surface dissolved oxygen and salinity were evident. Conversely, analysis of 111,243 neutral SNP markers revealed a lack of regional population differentiation, a finding that remained consistent across various analytical approaches. These results provide evidence for the presence of differential selection pressures within a limited spatial range, despite high gene flow implied by the selectively neutral dataset. This study offers notable insights regarding the potential impacts of genomic variation in response to fluctuating environmental conditions in the circumglobally distributed Sphyrna zygaena.