Genetic differentiation, effective population size and gene flow in marine fishes : implications for stock management

Many commercially exploited marine fish and mollusc species exhibit no or a low degree of genetic differentiation in neutral marker genes. This lack of genetic differentiation, typically attributed to high degree of gene flow in marine environments, has sometimes supported the thinking that genetically indistinguishable stocks can be managed as being one panmictic population. Recent comparative studies of neutral marker gene and quantitative trait differentiation in a wide variety of taxa - including several marine organisms - show that a high degree of genetic differentiation (as measured by Q_) in ecologically and economically important traits is a common place occurrence, even when the degree of differentiation in neutral marker genes (as measured by F_) is low or absent. In fact, among the empirical studies made so far, the outcome Q_>F_ is pervasive. This accords with the increasing evidence that natal homing and self-replenishment of local populations may be more common in marine habitats than previously anticipated. If so, the low degree of genetic differentiation in neutral genetic markers could be a simple consequence of the large effective population size (N_e) of many marine populations, effectively buffering them against differentiation due to genetic drift. However, genetic markers linked to parts of the genome under directional selection should readily diverge in allele frequencies especially when N_e is high. In fact, several recent studies have discovered that such loci provide a way to differentiate among stocks undifferentiated in neutral marker genes. Hence, the study of adaptive rather than neutral genetic differentiation among fish and shellfish populations might provide practical tools for stock identification and thereby contribute to improved fisheries policies.Special Revie

Complete mitochondrial genomes of the smooth tail nine-spined sticklebacks Pungitius laevis (Gasterosteiformes, Gasterosteidae)

Peer reviewe

Molecular sexing and population genetic inference using a sex-linked microsatellite marker in the nine-spined stickleback (Pungitius pungitius)

Peer reviewe

Construction of Ultradense Linkage Maps with Lep-MAP2 : Stickleback F-2 Recombinant Crosses as an Example

High-density linkage maps are important tools for genome biology and evolutionary genetics by quantifying the extent of recombination, linkage disequilibrium, and chromosomal rearrangements across chromosomes, sexes, and populations. They provide one of the best ways to validate and refine de novo genome assemblies, with the power to identity errors in assemblies increasing with marker density. However, assembly of high-density linkage maps is still challenging due to software limitations. We describe Lep-MAP2, a software for ultradense genome-wide linkage map construction. Lep-MAP2 can handle various family structures and can account for achiasmatic meiosis to gain linkage map accuracy. Simulations show that Lep-MAP2 outperforms other available mapping software both in computational efficiency and accuracy. When applied to two large F-2-generation recombinant crosses between two nine-spined stickleback (Pungitius pungitius) populations, it produced two high-density (similar to 6 markers/cM) linkage maps containing 18,691 and 20,054 single nucleotide polymorphisms. The two maps showed a high degree of synteny, but female maps were 1.5-2 times longer than male maps in all linkage groups, suggesting genome-wide recombination suppression in males. Comparison with the genome sequence of the three-spined stickleback (Gasterosteus aculeatus) revealed a high degree of interspecific synteny with a low frequency (Peer reviewe

High levels of fluctuating asymmetry in isolated stickleback populations

Background Fluctuating asymmetry (FA), defined as small random deviations from the ideal bilateral symmetry, has been hypothesized to increase in response to both genetic and environmental stress experienced by a population. We compared levels of FA in 12 bilateral meristic traits (viz. lateral-line system neuromasts and lateral plates), and heterozygosity in 23 microsatellite loci, among four marine (high piscine predation risk) and four pond (zero piscine predation risk) populations of nine-spined sticklebacks (Pungitius pungitius). Results Pond sticklebacks had on average three times higher levels of FA than marine fish and this difference was highly significant. Heterozygosity in microsatellite markers was on average two times lower in pond (HE ≈ 0.3) than in marine (HE ≈ 0.6) populations, and levels of FA and heterozygosity were negatively correlated across populations. However, after controlling for habitat effect on heterozygosity, levels of FA and heterozygosity were uncorrelated. Conclusions The fact that levels of FA in traits likely to be important in the context of predator evasion were elevated in ponds compared to marine populations suggests that relaxed selection for homeostasis in ponds lacking predatory fish may be responsible for the observed habitat difference in levels of FA. This inference also aligns with the observation that the levels of genetic variability across the populations did not explain population differences in levels of FA after correcting for habitat effect. Hence, while differences in strength of selection, rather than in the degree of genetic stress could be argued to explain habitat differences in levels of FA, the hypothesis that increased FA in ponds is caused by genetic stress cannot be rejected.Peer reviewe

Geographic Variation in Age Structure and Longevity in the Nine-Spined Stickleback (Pungitius pungitius)

Peer reviewe

Complete mitochondrial genome of the Sakhalin nine-spined stickleback Pungitius tymensis (Gasterosteiformes, Gasterosteidae)

Peer reviewe