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The species-rich genusMustelus(smoothhounds) of the shark family Triakidae is one of the most bio-economically important groups of elasmobranchs in the world’s oceans. Despite the commercial value ofMustelus, the systematics of the group remains largely unresolved and there is no global review or synthesis of knowledge about the conservation status and conservation genetics of smoothhounds across all oceanic regions. Here, we analysed published studies as well as grey literature to gain insight into the biogeographic, ecological and behavioural factors that shape genetic diversity in smoothhounds, and we identify critical knowledge gaps. From a series of molecular phylogenetic studies it can be inferred that the genusMustelusis paraphyletic and that the aplacental species evolved secondarily from the placental species of the genus. The increasing availability of genetic data aids in disentangling systematic issues, such that more meaningful morphological characters can be chosen for use in practical field-identification keys for co-occurring smoothhounds. An integrative taxonomic approach to the genusMustelusmay offer the best chance of recording and protecting the biodiversity of these sharks. Furthermore, it is evident that different smoothhound species exhibit unique gene-flow patterns, suggesting varying rates within species and hence that species-level conservation approaches would be most appropriate. Molecular studies have advanced our understanding of smoothhound biology (including reproductive traits), ecology and evolution. While many knowledge gaps remain, a crucial lesson from this review is that, when doing assessments on a molecular level, it is important to place genetic results in a broader context, by assimilating biological and ecological data, if definitive conclusions are to be drawn. [ABSTRACT FROM PUBLISHER]

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 ., Competing Interests: The authors declare no conflicts of interest., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)

Here, we present, for the first time, the Ion Torrent Ⓡ next-generation sequencing (NGS) data for five houndsharks (Chondrichthyes: Triakidae), which include Galeorhinus galeus (number of bases pairs (bp) 17,487; GenBank accession number ON652874), Mustelus asterias (16,708; ON652873), Mustelus mosis (16,755; ON075077), Mustelus palumbes (16,708; ON075076), and Triakis megalopterus (16,746; ON075075). All assembled mitogenomes encode 13 protein-coding genes (PCGs), two ribosomal (r)RNA genes, and 22 transfer (t)RNA genes ( tRNA Leu and tRNA Ser are duplicated), except for G. galeus which contains 23 tRNA genes where tRNA Thr is duplicated. The data presented in this paper can assist other researchers in further elucidating the diversification of triakid species and the phylogenetic relationships within Carcharhiniformes (groundsharks) as mitogenomes accumulate in public repositories., (© 2024 The Author(s).)

Background: The order Lepidoptera has an abundance of species, including both agriculturally beneficial and detrimental insects. Molecular data has been used to investigate the phylogenetic relationships of major subdivisions in Lepidoptera, which has enhanced our understanding of the evolutionary relationships at the family and superfamily levels. However, the phylogenetic placement of many superfamilies and/or families in this order is still unknown. In this study, we determine the systematic status of the family Argyresthiidae within Lepidoptera and explore its phylogenetic affinities and implications for the evolution of the order. We describe the first mitochondrial (mt) genome from a member of Argyresthiidae, the apple fruit moth Argyresthia conjugella. The insect is an important pest on apples in Fennoscandia, as it switches hosts when the main host fails to produce crops., Results: The mt genome of A. conjugella contains 16,044 bp and encodes all 37 genes commonly found in insect mt genomes, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and a large control region (1101 bp). The nucleotide composition was extremely AT-rich (82%). All detected PCGs (13) began with an ATN codon and terminated with a TAA stop codon, except the start codon in cox1 is ATT. All 22 tRNAs had cloverleaf secondary structures, except trnS1, where one of the dihydrouridine (DHU) arms is missing, reflecting potential differences in gene expression. When compared to the mt genomes of 507 other Lepidoptera representing 18 superfamilies and 42 families, phylogenomic analyses found that A. conjugella had the closest relationship with the Plutellidae family (Yponomeutoidea-super family). We also detected a sister relationship between Yponomeutoidea and the superfamily Tineidae., Conclusions: Our results underline the potential importance of mt genomes in comparative genomic analyses of Lepidoptera species and provide valuable evolutionary insight across the tree of Lepidoptera species., (© 2023. The Author(s).)

The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly and paraphyly within the family. We hypothesize that this variability is triggered by the selection of different a priori partitioning schemes to account for site and gene heterogeneity within the mitogenome. Here we used an extensive statistical framework to select the a priori partitioning scheme for inference of the mitochondrial phylogenomic relationships within Carcharhiniformes, tested site heterogeneous CAT + GTR + G4 models and incorporated the multi-species coalescent model (MSCM) into our analyses to account for the influence of gene tree discordance on species tree inference. We included five newly assembled houndshark mitogenomes to increase resolution of Triakidae. During the assembly procedure, we uncovered a 714 bp-duplication in the mitogenome of Galeorhinus galeus. Phylogenetic reconstruction confirmed monophyly within Triakidae and the existence of two distinct clades of the expanded Mustelus genus. The latter alludes to potential evolutionary reversal of reproductive mode from placental to aplacental, suggesting that reproductive mode has played a role in the trajectory of adaptive divergence. These new sequences have the potential to contribute to population genomic investigations, species phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies for these ecologically and economically important species., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Inc.)

Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene-environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark ( Carcharhinus brachyurus ) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype-environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations., Competing Interests: The authors declare no conflicts of interest., (© 2023 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Studies on host-parasite systems that have experienced distributional shifts, range fragmentation, and population declines in the past can provide information regarding how parasite community richness and genetic diversity will change as a result of anthropogenic environmental changes in the future. Here, we studied how sequential postglacial colonization, shifts in habitat, and reduced host population sizes have influenced species richness and genetic diversity of Corynosoma (Acanthocephala: Polymorphidae) parasites in northern European marine, brackish, and freshwater seal populations. We collected Corynosoma population samples from Arctic, Baltic, Ladoga, and Saimaa ringed seal subspecies and Baltic gray seals, and then applied COI barcoding and triple-enzyme restriction-site associated DNA (3RAD) sequencing to delimit species, clarify their distributions and community structures, and elucidate patterns of intraspecific gene flow and genetic diversity. Our results showed that Corynosoma species diversity reflected host colonization histories and population sizes, with four species being present in the Arctic, three in the Baltic Sea, two in Lake Ladoga, and only one in Lake Saimaa. We found statistically significant population-genetic differentiation within all three Corynosoma species that occur in more than one seal (sub)species. Genetic diversity tended to be high in Corynosoma populations originating from Arctic ringed seals and low in the landlocked populations. Our results indicate that acanthocephalan communities in landlocked seal populations are impoverished with respect to both species and intraspecific genetic diversity. Interestingly, the loss of genetic diversity within Corynosoma species seems to have been less drastic than in their seal hosts, possibly due to their large local effective population sizes resulting from high infection intensities and effective intra-host population mixing. Our study highlights the utility of genomic methods in investigations of community composition and genetic diversity of understudied parasites., Competing Interests: The authors declare no conflicts of interest., (© 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Aquaculture of the lumpfish ( Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for "cleaner fish" to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the spatial patterns of genomic variation in the lumpfish along the coast of Norway and across the North Atlantic. Moreover, we applied three genome scans for outliers and two genotype-environment association tests to assess the signatures and patterns of local adaptation under extensive gene flow. With our 'global' sampling regime, we found two major genetic groups of lumpfish, i.e., the western and eastern Atlantic. Regionally in Norway, we found marginal evidence of population structure, where the population genomic analysis revealed a small portion of individuals with a different genetic ancestry. Nevertheless, we found strong support for local adaption under high gene flow in the Norwegian lumpfish and identified over 380 high-confidence environment-associated loci linked to gene sets with a key role in biological processes associated with environmental pressures and embryonic development. Our results bridge population genetic/genomics studies with seascape genomics studies and will facilitate genome-enabled monitoring of the genetic impacts of escapees and allow for genetic-informed broodstock selection and management in Norway.

We determined the mitogenome of Cyclopterus lumpus using a hybrid sequencing approach, and another four closely related species in the Liparidae based on available next-generation sequence data. We found that the mitogenome of C. lumpus was 17,266 bp in length, where the length and organisation were comparable to those reported for cottoids. However, we found a GC-homopolymer region in the intergenic space between tRNA Leu2 and ND1 in liparids and cyclopterids. Phylogenetic reconstruction confirmed the monophyly of infraorders and firmly supported a sister-group relationship between Cyclopteridae and Liparidae. Purifying selection was the predominant force in the evolution of cottoid mitogenomes. There was significant evidence of relaxed selective pressures along the lineage of deep-sea fish, while selection was intensified in the freshwater lineage. Overall, our analysis provides a necessary expansion in the availability of mitogenomic sequences and sheds light on mitogenomic adaptation in Cottoidei fish inhabiting different aquatic environments., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

The common smooth-hound shark, Mustelus mustelus, is a widely distributed demersal shark under heavy exploitation from various fisheries throughout its distribution range. To assist in the development of appropriate management strategies, the authors evaluate stock structure, site fidelity and movement patterns along the species' distribution in southern Africa based on a combination of molecular and long-term tag-recapture data. Eight species-specific microsatellite markers (N = 73) and two mitochondrial genes, nicotinamide adenine dehydrogenase subunit 4 and control region (N = 45), did not reveal any significant genetic structure among neighbouring sites. Nonetheless, tagging data demonstrate a remarkable degree of site fidelity with 76% of sharks recaptured within 50 km of the original tagging location. On a larger geographic scale, dispersal is governed by oceanographic features as demonstrated by the lack of movements across the Benguela-Agulhas transition zone separating the South-East Atlantic Ocean (SEAO) and South-West Indian Ocean (SWIO) populations. Microsatellite data supported very shallow ocean-based structure (SEAO and SWIO) and historical southward gene flow following the Agulhas Current, corroborating the influence of this dynamic oceanographic system on gene flow. Moreover, no movements between Namibia and South Africa were observed, indicating that the Lüderitz upwelling formation off the Namibian coast acts as another barrier to dispersal and gene flow. Overall, these results show that dispersal and stock structure of M. mustelus are governed by a combination of behavioural traits and oceanographic features such as steep temperature gradients, currents and upwelling systems., (© 2021 Fisheries Society of the British Isles.)

Loss of Arctic sea ice owing to climate change is predicted to reduce both genetic diversity and gene flow in ice-dependent species, with potentially negative consequences for their long-term viability. Here, we tested for the population-genetic impacts of reduced sea ice cover on the polar bear ( Ursus maritimus ) sampled across two decades (1995-2016) from the Svalbard Archipelago, Norway, an area that is affected by rapid sea ice loss in the Arctic Barents Sea. We analysed genetic variation at 22 microsatellite loci for 626 polar bears from four sampling areas within the archipelago. Our results revealed a 3-10% loss of genetic diversity across the study period, accompanied by a near 200% increase in genetic differentiation across regions. These effects may best be explained by a decrease in gene flow caused by habitat fragmentation owing to the loss of sea ice coverage, resulting in increased inbreeding of local polar bears within the focal sampling areas in the Svalbard Archipelago. This study illustrates the importance of genetic monitoring for developing adaptive management strategies for polar bears and other ice-dependent species.

Maintaining standing genetic variation is a challenge in human-dominated landscapes. We used genetic (i.e., 16 short tandem repeats) and morphological (i.e., length and weight) measurements of 593 contemporary and historical brown trout (Salmo trutta) samples to study fine-scale and short-term impacts of different management practices. These had changed from traditional breeding practices, using the same broodstock for several years, to modern breeding practices, including annual broodstock replacement, in the transnational subarctic Pasvik River. Using population genetic structure analyses (i.e., Bayesian assignment tests, DAPCs, and PCAs), four historical genetic clusters (E2001A-D), likely representing family lineages resulting from different crosses, were found in zone E. These groups were characterized by consistently lower genetic diversity, higher within-group relatedness, lower effective population size, and significantly smaller body size than contemporary stocked (E2001E) and wild fish (E2001F). However, even current breeding practices are insufficient to prevent genetic diversity loss and morphological changes as demonstrated by on average smaller body sizes and recent genetic bottleneck signatures in the modern breeding stock compared to wild fish. Conservation management must evaluate breeding protocols for stocking programs and assess if these can preserve remaining natural genetic diversity and morphology in brown trout for long-term preservation of freshwater fauna., (© 2021. The Author(s).)

Conservation and management of large carnivores requires knowledge of female and male dispersal. Such information is crucial to evaluate the population's status and thus management actions. This knowledge is challenging to obtain, often incomplete and contradictory at times. The size of the target population and the methods applied can bias the results. Also, population history and biological or environmental influences can affect dispersal on different scales within a study area. We have genotyped Eurasian lynx (180 males and 102 females, collected 2003-2017) continuously distributed in southern Finland (~23,000 km2) using 21 short tandem repeats (STR) loci and compared statistical genetic tests to infer local and sex-specific dispersal patterns within and across genetic clusters as well as geographic regions. We tested for sex-specific substructure with individual-based Bayesian assignment tests and spatial autocorrelation analyses. Differences between the sexes in genetic differentiation, relatedness, inbreeding, and diversity were analysed using population-based AMOVA, F-statistics, and assignment indices. Our results showed two different genetic clusters that were spatially structured for females but admixed for males. Similarly, spatial autocorrelation and relatedness was significantly higher in females than males. However, we found weaker sex-specific patterns for the Eurasian lynx when the data were separated in three geographical regions than when divided in the two genetic clusters. Overall, our results suggest male-biased dispersal and female philopatry for the Eurasian lynx in Southern Finland. The female genetic structuring increased from west to east within our study area. In addition, detection of male-biased dispersal was dependent on analytical methods utilized, on whether subtle underlying genetic structuring was considered or not, and the choice of population delineation. Conclusively, we suggest using multiple genetic approaches to study sex-biased dispersal in a continuously distributed species in which population delineation is difficult., Competing Interests: The authors have declared that no competing interests exist.

The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the economic importance, few genetic resources for downstream applications, such as linkage mapping, parentage analysis, marker-assisted selection (MAS), quantitative trait loci (QTL) analysis, and assessing adaptive genetic diversity are currently available for the species. Here, we identify both genome- and transcriptome-derived microsatellites loci from C. lumpus to facilitate such applications. Across 2,346 genomic contigs, we detected a total of 3,067 microsatellite loci, of which 723 were the most suitable ones for primer design. From 116,555 transcriptomic unigenes, we identified a total of 231,556 microsatellite loci, which may indicate a high coverage of the available STRs. Out of these, primer pairs could only be designed for 6,203 loci. Dinucleotide repeats accounted for 89 percent and 52 percent of the genome- and transcriptome-derived microsatellites, respectively. The genetic composition of the dominant repeat motif types showed differences from other investigated fish species. In the genome-derived microsatellites AC/GT (67.8 percent), followed by AG/CT (15.1 percent) and AT/AT (5.6 percent) were the major motifs. Transcriptome-derived microsatellites showed also most dominantly the AC/GT repeat motif (33 percent), followed by A/T (26.6 percent) and AG/CT (11 percent). Functional annotation of microsatellite-containing transcriptomic sequences showed that the majority of the expressed sequence tags encode proteins involved in cellular and metabolic processes, binding activity and catalytic reactions. Importantly, STRs linked to genes involved in immune system process, growth, locomotion and reproduction were discovered in the present study. The extensive genomic marker information reported here will facilitate molecular ecology studies, conservation initiatives and will benefit many aspects of the breeding programmes of C. lumpus.

Habitat discontinuity, anthropogenic disturbance, and overharvesting have led to population fragmentation and decline worldwide. Preservation of remaining natural genetic diversity is crucial to avoid continued genetic erosion. Brown trout ( Salmo trutta L.) is an ideal model species for studying anthropogenic influences on genetic integrity, as it has experienced significant genetic alterations throughout its natural distribution range due to habitat fragmentation, overexploitation, translocations, and stocking. The Pasvik River is a subarctic riverine system shared between Norway, Russia, and Finland, subdivided by seven hydroelectric power dams that destroyed about 70% of natural spawning and nursing areas. Stocking is applied in certain river parts to support the natural brown trout population. Adjacent river segments with different management strategies (stocked vs. not stocked) facilitated the simultaneous assessment of genetic impacts of dams and stocking based on analyses of 16 short tandem repeat loci. Dams were expected to increase genetic differentiation between and reduce genetic diversity within river sections. Contrastingly, stocking was predicted to promote genetic homogenization and diversity, but also potentially lead to loss of private alleles and to genetic erosion. Our results showed comparatively low heterozygosity and clear genetic differentiation between adjacent sections in nonstocked river parts, indicating that dams prevent migration and contribute to genetic isolation and loss of genetic diversity. Furthermore, genetic differentiation was low and heterozygosity relatively high across stocked sections. However, in stocked river sections, we found signatures of recent bottlenecks and reductions in private alleles, indicating that only a subset of individuals contributes to reproduction, potentially leading to divergence away from the natural genetic state. Taken together, these results indicate that stocking counteracts the negative fragmentation effects of dams, but also that stocking practices should be planned carefully in order to ensure long-term preservation of natural genetic diversity and integrity in brown trout and other species in regulated river systems., Competing Interests: None declared.

The non-model shark species, dusky shark Carcharhinus obscurus, is a bio-economically and recreationally important shark in many areas of its range. Despite of the fishery importance of C. obscurus few genetic resources are currently available for the species. Here, we report on the isolation of eight novel microsatellite loci from C. obscurus using a double-digest restriction site associated DNA (RAD) sequencing approach on the Ion Proton semiconductor platform (ddRADseq-ion). We characterised the loci in 26 individuals and all loci were polymorphic, exhibiting 5-10 alleles (average 6.6), and observed and expected heterozygosities of 0.385-0.962 and 0.479-0.847, respectively. We found that all pairs of loci were in linkage equilibrium and conformed to Hardy-Weinberg expectations. The loci reported in this study are only the second set of microsatellite loci ever characterized for C. obscurus and will be valuable for molecular ecology studies for this vulnerable species.

We present the complete mitochondrial genome of the common smoothhound , Mustelus mustelus, which is 16,755 bp long, contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and non-coding control region. All protein-coding genes begin with the ATG codon, except for the COI gene, which begins with GTG. Six protein-coding genes terminated with the TAA codon, and six with incomplete codons, T or TA. The phylogenetic reconstruction places M . mustelus within the genus Mustelus , with the closest relationship to the placental species, M . griseus . This mitogenome provides valuable information to further unravel the evolution of alternate reproductive modes within the genus., Competing Interests: The authors declare no conflict of interest and were solely responsible for the content and writing of this paper., (© 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The present histological study of adult female common smoothhound shark Mustelus mustelus demonstrates that the species can store sperm in their oviducal glands. In addition, single paternity of a litter of 22 pups is reported, contributing to further knowledge regarding the genetic and behavioural mating strategy of M. mustelus., (© 2018 The Fisheries Society of the British Isles.)

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.

Background: Similarly to the rest of the world, southern Africa's diverse chondrichthyan fauna is currently experiencing high fishing pressures from direct and non-direct fisheries to satisfy market demands for shark products such as fins and meat. In this study, the development of microsatellite markers through cross-species amplification of primer sets previously developed for closely related species is reported as an alternative approach to de novo marker development. This included the design of four microsatellite multiplex assays and their cross-species utility in genetic diversity analysis of southern African elasmobranchs. As this study forms part of a larger project on the development of genetic resources for commercially important and endemic southern African species, Mustelus mustelus was used as a candidate species for testing these multiplex assays in down-stream applications., Results: Thirty five microsatellite primer sets previously developed for five elasmobranch species were selected from literature for testing cross-species amplification in 16 elasmobranch species occurring in southern Africa. Cross-species amplification success rates ranged from 28.6%-71.4%. From the successfully amplified microsatellites, 22 loci were selected and evaluated for levels of polymorphism, and four multiplex assays comprising of the 22 microsatellites were successfully constructed, optimised and characterised in a panel of 87 Mustelus mustelus individuals. A total of 125 alleles were observed across all loci, with the number of alleles ranging from 3-12 alleles. Cross-species amplification of the four optimised multiplex assays was further tested on 11 commercially important and endemic southern African elasmobranch species. Percentage of polymorphism ranged from 31.8%-95.5% in these species with polymorphic information content decreasing exponentially with evolutionary distance from the source species., Conclusions: Cross-species amplification of the 35 microsatellites proved to be a time- and cost-effective approach to marker development in elasmobranchs and enabled the construction of four novel multiplex assays for characterising genetic diversity in a number of southern African elasmobranch species. This study successfully demonstrated the usefulness of these markers in down-stream applications such as genetic diversity assessment and species identification which could potentially aid in a more integrative, multidisciplinary approach to management and conservation of commercially important cosmopolitan and endemic elasmobranch species occurring in southern Africa.

Haliotis midae is South Africa's most important aquaculture species. The reproduction cycle is currently not closed as many farms rely on wild-caught broodstock for seed production. However, there is an increasing interest in genetic improvement in commercial stocks, with a growing number of producers implementing selective breeding strategies. High throughput commercial production and mass spawning make it difficult to maintain breeding records; therefore, mostly mass selection is practised. The high fecundity and unequal parental contributions also often lead to increased levels of inbreeding. This study therefore aimed to assess the genetic effects of such breeding practices on commercial populations of H. midae. Using microsatellite loci, the genetic properties of a wild, an F1 and an F2 population were estimated and compared. Although there was no significant loss of genetic diversity amongst the cultured populations in comparison with the wild progenitor population, there was low-to-moderate genetic differentiation between populations. Relatedness amongst the F2 population was significant, and the rate of inbreeding was high. The effective population size for the F2 (±50) was also comparatively small with respect to the wild (∞) and F1 (±470) populations. These results suggest that farms need to give caution to breeding practices beyond the first (F1) generation and aim to increase effective population sizes and minimise inbreeding to ensure long-term genetic gain and productivity. This study also confirms the usefulness of population genetic analyses for commercial breeding and stock management in the absence of extensive pedigree records., (© 2014 Stichting International Foundation for Animal Genetics.)