Evaluating genetic traceability methods for captive bred marine fish and their applications in fisheries management and wildlife forensics

Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in the aquaculture production. Consequently, more captive bred fish are released into the wild through accidental escape or deliberate restocking, stock enhancement and sea ranching programs. The increased mixing of captive bred fish with wild conspecifics may affect the ecological and/or genetic integrity of wild fish populations. From a fisheries management perspective unambiguous identification tools for captive bred fish will be highly valuable to manage risks. Additionally there is great potential to use these tools in wildlife forensics (i.e. tracing back escapees to their origin and determining mislabelling of seafood products). Using SNP data from captive bred and wild populations of Atlantic cod (Gadus morhua L.) and sole (Solea solea L.), we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterizes the broodstock and escapees originate from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case by case strategy when choosing the best method

Parentage assignment with genomic markers: a major advance for understanding and exploiting genetic variation of quantitative traits in farmed aquatic animals

Since the middle of the 1990s, parentage assignment using microsatellite markers has been introduced as a tool in aquaculture breeding. It now allows close to 100% assignment success, and offered new ways to develop aquaculture breeding using mixed family designs in commercial conditions. Its main achievements are the knowledge and control of family representation and inbreeding, especially in mass spawning species, above all the capacity to estimate reliable genetic parameters in any species and rearing system with no prior investment in structures, and the development of new breeding programs in many species. Parentage assignment should not be seen as a way to replace physical tagging, but as a new way to conceive breeding programs, which have to be optimized with its specific constraints, one of the most important being to well define the number of individuals to genotype to limit costs, maximize genetic gain while minimizing inbreeding. The recent possible shift to (for the moment) more costly single nucleotide polymorphism markers should benefit from future developments in genomics and marker-assisted selection to combine parentage assignment and indirect prediction of breeding values

Short Tandem Repeat-based Identification of Individuals and Parents

Estimation of short tandem repeat (STR) multilocus genotype frequencies for the identification of individuals and estimation of allele frequencies for parentage assignment both depend on (a) testing a lot of loci, (b) high levels of polymorphism at each locus tested, and (c) independence among alleles. Independence is critical, because the estimation of multilocus genotype and gamete frequencies is based on multiplying individual allele frequencies to produce a composite frequency estimate. Independence among alleles at a locus is known as Hardy-Weinberg equilibrium, whereas allelic independence between loci is known as linkage equilibrium. The frequency at which individual identification may be declared is a matter of opinion, as there is no scientific way to specify certainty based on frequency estimates. Similarly absolute assignment of parentage is impossible in theory; in practice it is more difficult than individual identification, because only half as much information is available (gamete vs genotype frequency) and because mutation may confound parentage analysis

Low-density genotype panel for both parentage verification and discovery in a multi-breed sheep population

peer-reviewedThe generally low usage of artificial insemination and single-sire mating in sheep, compounded by mob lambing (and lambing outdoors), implies that parentage assignment in sheep is challenging. The objective here was to develop a low-density panel of single nucleotide polymorphisms (SNPs) for accurate parentage verification and discovery in sheep. Of particular interest was where SNP selection was limited to only a subset of chromosomes, thereby eliminating the ability to accurately impute genome-wide denser marker panels. Data used consisted of 10,933 candidate SNPs on 9,390 purebred sheep. These data consisted of 1,876 validated genotyped sire–offspring pairs and 2,784 validated genotyped dam–offspring pairs. The SNP panels developed consisted of 87 SNPs to 500 SNPs. Parentage verification and discovery were undertaken using 1) exclusion, based on the sharing of at least one allele between candidate parent–offspring pairs, and 2) a likelihood-based approach. Based on exclusion, allowing for one discordant offspring–parent genotype, a minimum of 350 SNPs was required when the goal was to unambiguously identify the true sire or dam from all possible candidates. Results suggest that, if selecting SNPs across the entire genome, a minimum of 250 carefully selected SNPs are required to ensure that the most likely selected parent (based on the likelihood approach) was, in fact, the true parent. If restricting the SNPs to just a subset of chromosomes, the recommendation is to use at least a 300-SNP panel from at least six chromosomes, with approximately an equal number of SNPs per chromosome

Statistical methods for detecting genes associated with sperm competition in natural populations of Drosophila, using blocks of tightly linked single nucleotide polymorphisms : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Statistics at Massey University, Albany, New Zealand

The purpose of the project is to develop statistical methods for detecting genes associated with sperm competition in natural populations of Drosophila (fruit flies). The flies' genotype information given by Fiumera et al. (2004) is used as the starting point of the analysis. This dataset utilizes blocks of tightly linked single nucleotide polymorphisms within genes suspected to affect sperm competition. The sperm competition detection process is completed in three different stages: maternal and offspring haplotypes reconstruction; paternal genotype and offspring fraction estimation; and preferred genotype detection. Software programs HAPLORE and PHASE 2.0 were implemented for maternal and offspring haplotype reconstruction. The software Parentage is applied on the reconstructed haplotypes for estimating paternal genotypes and the amount of offspring they produced. Lastly, the Kruskal Wallis and permutation tests were conducted to detect differences in offspring produced between groups of males with different genotypes

Environmental, social, morphological, and behavioral constraints on opportunistic multiple paternity

Peer reviewedPostprin

A common garden design reveals population-specific variability in potential impacts of hybridisation between populations of farmed and wild Atlantic salmon, Salmo salar L

Released individuals can have negative impacts on native populations through various mechanisms; including competition, disease transfer and introduction of maladapted gene-complexes. Previous studies indicate that the level of farmed Atlantic salmon introgression in native populations is population-specific. However few studies have explored the potential role of population diversity or river characteristics, such as temperature, on the consequences of hybridisation. We compared freshwater growth of multiple families derived from two farmed, five wild, and two F1 hybrid salmon populations at three contrasting temperatures (7°C, 12°C, and 16°C) in a common garden experiment. As expected, farmed salmon outgrew wild salmon at all temperatures, with hybrids displaying intermediate growth. However, differences in growth were population-specific and some wild populations performed better than others relative to the hybrid and farmed populations at certain temperatures. Therefore, the competitive balance between farmed and wild salmon may depend both on the thermal profile of the river and the genetic characteristics of the respective farmed and wild strains. While limited to F1 hybridisation, the present study shows the merits in adopting a more complex spatially resolved approach to risk management of local populations

AFLPs: genetic markers for paternity studies in newts (Triturus vulgaris)

DNA-based genetic markers can reveal paternity whenever the direct assignment of fathers to offspring is precluded by multiple matings and internal fertilisation. Microsatellites are the current marker of choice in many behavioural studies, and have revealed important insights into genetic mating systems of European amphibians. However, the number of amphibian species for which the time-consuming designing of locus-specific microsatellite primers was successful is still limited, and the cross-utilisation of existing markers to closely related taxa seems to have a particularly low success rate. Allozymes can infer parentage without a species-specific protocol, but, due to their low degree of polymorphism, in mate choice experiments require the a priori screening of individuals. Dominant markers such as RAPDs successfully identified closely-related amphibian species and their hybrids, but might be less suited to distinguish between closely related individuals with a putatively high frequency of shared bands

SNP Miniplexes for Individual Identification of Random-Bred Domestic Cats.

Phenotypic and genotypic characteristics of the cat can be obtained from single nucleotide polymorphisms (SNPs) analyses of fur. This study developed miniplexes using SNPs with high discriminating power for random-bred domestic cats, focusing on individual and phenotypic identification. Seventy-eight SNPs were investigated using a multiplex PCR followed by a fluorescently labeled single base extension (SBE) technique (SNaPshot(®) ). The SNP miniplexes were evaluated for reliability, reproducibility, sensitivity, species specificity, detection limitations, and assignment accuracy. Six SNPplexes were developed containing 39 intergenic SNPs and 26 phenotypic SNPs, including a sex identification marker, ZFXY. The combined random match probability (cRMP) was 6.58 × 10(-19) across all Western cat populations and the likelihood ratio was 1.52 × 10(18) . These SNPplexes can distinguish individual cats and their phenotypic traits, which could provide insight into crime reconstructions. A SNP database of 237 cats from 13 worldwide populations is now available for forensic applications